Method for using and making a fiber array

ABSTRACT

The invention provides a method for contacting at least two chemical species by immobilizing an immobilized chemical species on a fiber, placing the fiber on a support having a channel, and disposing a mobile chemical species into the channel such that the immobilized chemical species contacts the fiber. The invention also provides methods for analyzing the contact between at least two chemical species, detecting the binding of two chemical species, making a microchip, and synthesizing a chemical species on a fiber.

This is a division of application Ser. No. 09/479,181, filed Jan. 7,2000.

This is a continuation-in-part of application Ser. No. 09/227,799, filedJan. 8, 1999, now abandoned.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The invention relates generally to micro-arrays for contacting smallquantities of chemical species. More specifically, the invention relatesto micro-arrays for contacting an oligonucleotide probe with anoligonucleotide target, a reader for reading the micro-array, and amethod and apparatus for making the micro-array.

2. Description of Related Art

Presently, micro-arrays are being used for a wide range of applicationssuch as gene discovery, disease diagnosis, drug discovery(pharmacogenomics) and toxicological research (toxicogenomics). Amicro-array is an orderly arrangement of immobilized chemical compounds.Micro-arrays provide a medium for matching known and unknown DNA samplesbased on base-pairing rules. The typical method involves contacting anarray of immobilized chemical compounds with a target of interest toidentify those compounds in the array that bind to the target. Arraysare generally described as macro-arrays or micro-arrays, the differencebeing the size of the sample spots. Macro-arrays contain sample spotsizes of about 300 microns or larger whereas micro-arrays are typicallyless than 200 microns in diameter and typically contain thousands ofspots.

DNA micro-arrays, or DNA (gene) chips are typically fabricated byhigh-speed robotics on glass or nylon substrates, for which probes withknown identity are used to determine complementary binding. A “probe” isa tethered nucleic acid with known sequence, whereas a “target” is thefree nucleic acid sample whose identity is being detected.

One array-based application that requires very high density miniaturizedarrays is sequencing by hybridization (SBH). In one common format of SBH(format II), a spatially-addressable array of the complete set ofoligonucleotide probes of length n is constructed. The oligonucleotideprobes are typically covalently attached to a flat, solid substrate,such as a glass slide. Each address in the array has a unique n-merattached thereto, and the sequence of the probe is defined by itsspatial address (xy coordinates). The array is contacted with a labeledtarget nucleic acid under conditions which discriminate between theformation of perfectly complementary probe-target hybrids and hybridscontaining mismatches. Thus, only those addresses of the array whichhave attached thereto oligonucleotide probes that are completelycomplementary to a portion of the target nucleic acid produce a signal.The array is then scanned for signals, the sequences of complementaryprobes determined from their spatial addresses, and the sequence of thetarget nucleic acid determined by overlapping the common sequences ofthe probes.

Two other SBH formats also exist. In format I SBH, the target nucleicacid is immobilized on a solid support, e.g., a nylon or nitrocellulosefilter, and the immobilized target interrogated with labeled probes.Typically, the target is interrogated with a single probe at a time, oralternatively with a plurality of probes, each of which bears adifferent distinguishable label (this latter mode is termed“multiplexing”). To reduce the number of manipulations required, thetarget nucleic acid can be spotted onto a filter in a grid or array, andeach spot or address in the array interrogated with a single probe orplurality of multiplexed probes.

In yet another format of SBH, (format III), an array of immobilizedoligonucleotide probes similar to that used for format II SBH iscontacted with an unlabeled target nucleic acid under conditions whichdiscriminate between perfectly complementary and mismatched hybrids. Thearray is then contacted with a labeled probe under conditions whichdiscriminate between perfectly complementary and mismatched labeledprobe target complexes. Following hybridization, the array is subjectedto conditions which covalently join probes which are hybridizedadjacently to the target (e.g., a ligase). The unligated labeled probe,and optionally target nucleic acid, is then washed away. The array isthen scanned for signal. Since the solution-phase probe was labeled,only those addresses where ligation took place produce a signal. Thesequence of the target nucleic acid is determined by overlapping thecommon sequences of the ligated probes.

For a review of the three types of SBH and their respective advantages,see U.S. Pat. Nos. 5,202,231; 5,525,464; WO 98/31836; WO 96/17957 andthe references cited therein.

The length of target nucleic acid which can be sequenced using SBHtechniques depends on the lengths of the oligonucleotide probes.Generally, sequencing a target nucleic acid a few hundred nucleotides inlength requires the oligonucleotide probes to be at least 8 nucleotidesin length. Sequencing longer target nucleic acids, or sequencing thoughregions of tandem repeats, requires even longer probes. Some haveestimated that sequencing a target nucleic acid over one thousandnucleotides in length would require oligonucleotide probes of at least12 to 14 nucleotides in length. Because the methods require the use ofcomplete sets of probes, i.e., every possible sequence of length n, theprobe sets required for the method are extremely large. For example, thecomplete set of 8-mer probes consists of 4⁸ or 65,356 unique sequences.The complete set of 10-mer probes consists of 4¹⁰ or 1,048,576 uniquesequences and the complete set of 14-mer probes consists of 4¹⁴ or268,435,456 unique sequences. In order to make the assays practical, theentire probe array must typically be on the order of 1 cm² in area.

To meet the needs of applications requiring high-density miniaturizedarrays of immobilized compounds, such as SBH and its relatedapplications, two general methods have been developed for synthesizingthe immobilized arrays: in situ methods in which each compound in thearray is synthesized directly on the surface of the substrate anddeposition methods in which pre-synthesized compounds capable of beingcovalently attached to the surface of the substrate are deposited,typically by way of robot dispensing devices, at the appropriate spatialaddresses. The in situ methods typically require specialized reagentsand complex masking strategies, and the deposition methods typicallyrequire precise robotic delivery of very defined quantities of reagents.

For example, Fodor et al., 1991, Science 251:767-773 describe an in situmethod which utilizes photo-protected amino acids and photo lithographicmasking strategies to synthesize miniaturized, spatially-addressablearrays of peptides. This in situ method has recently been expanded tothe synthesis of miniaturized arrays of oligonucleotides (U.S. Pat. No.5,744,305). Another in situ synthesis method for makingspatially-addressable arrays of immobilized oligonucleotides isdescribed by Southern, 1992, Genomics 13:1008-1017; see also Southern &Maskos, 1993, Nucl. Acids Res. 21:4663-4669; Southern & Maskos, 1992,Nucl. Acids Res. 20:1679-1684; Southern & Maskos, 1992, Nucl. Acids Res.20:1675-1678. In this method, conventional oligonucleotide synthesisreagents are dispensed onto physically masked glass slides to create thearray of immobilized oligonucleotides.

U.S. Pat. No. 5,807,522 describes a deposition method for making microarrays of biological samples that involves dispensing a known volume ofreagent at each address of the array by tapping a capillary dispenser onthe substrate under conditions effective to draw a defined volume ofliquid onto the substrate.

One of the biggest drawbacks of both the in situ and deposition microfabrication techniques is the inability to verify the integrity of thearray once it has been fabricated. Absent analyzing the compoundimmobilized at each address, the integrity of the deposition chemistrysimply cannot be verified. Such an analysis would be extremely laborintensive, and may even be impossible for extremely high-density arrays,as the quantity of compound immobilized may not be sufficient foranalysis and subsequent use.

Moreover, since each array is fabricated de novo, the integrity of eacharray synthesized is suspect. Without being able to verify that thearray has been fabricated with high fidelity, the absence of a signal ata particular address cannot be unambiguously interpreted. The absence ofsignal could be due to a failed synthesis or immobilization at thataddress.

Deposition methods suffer additional drawbacks, as well. Automaticdeposition generally uses a robotic fluid delivery system. The robotmoves to specific locations on the microcard, delivering a specifiedamount of fluid. The fluid is deposited onto the microcard by either anon-contact ejector (such as ink jet nozzles) or a contact ejector (suchas a pen, quill, or fiber) which actually touches the microcard surfaceto release the fluid. Ink jets, pens, and quills are adaptations ofcommon devices, and each have reliability problems. Ink jets work finewhen the fluid has been carefully optimized for the nozzle. However,when depositing many different fluids through the same nozzle,optimization of each fluid is impractical. Pens and quills are veryuseful for deposition onto a small number of plates but are too slow forcost-effective production. While a fiber piston delivery system showspromise as a reliable means of fluid deposition, it requires an unwieldynumber of fibers for a very large number of reaction sites.

In addition to problems with the reliability of ejectors, the total timeto deposit thousands of different probe fluids with existing automatedejector devices increases the cost of a microcard beyond the cost ofother approaches, i.e. the automated process is not cost-effective.Somewhat surprisingly, this is not due to the speed of fluid depositionby the robot, which is relatively fast. Rather, it is the combination ofother on-line procedures such as wicking, cleaning, and loading slidesthat makes the total deposition time unacceptable. To have thousands ofindependent probe liquids means that the robot can only deposit a fewspots on one slide (assuming some duplication) before it has to load(wick) another probe fluid into the reservoirs of its ejector or quill.Wicking usually involves providing an open vessel containing the probefluid such that the robot can move the ejector/quill into the fluid andload the fluid through vacuum or capillary action into a reservoir inthe ejector/quill. This process can take several seconds, and must beconducted whenever dispensing a new probe fluid. Also, beforeintroducing a new probe fluid, the ejector/quill must be cleaned toprevent contamination of the new probe fluid with the previous one. Thiscleaning usually involves flushing the ejector/quill with a cleaningsolvent and drying them with flowing gas. The cleaning process alsotakes several seconds and must be conducted whenever dispensing a newprobe fluid. Furthermore, the loading (and unloading) of slides into therobot's workspace also adds to the overall processing time. Sincewicking, cleaning, and loading are on-line procedures, they all add tothe total time of deposition. Spotting many slides at a time improvesthe robotic deposition time but still requires the same wicking andcleaning time before depositing a different fluid. Therefore, wicking,cleaning, and loading time alone make the process too time consuming andexpensive to consider as a viable alternative.

Consequently, neither in situ nor existing automated approaches are areliable or cost-effective means of mass-producing micro arrays.Therefore, there is a need for methods of making microarrays that avoidthe problems associated with currently available in situ and depositionmethods and which provide a matrix or array of contact points forcontacting small quantities of at least two chemical species.Furthermore, there is a need for a more advantageous structure for themicro arrays that can provide an increased number of mix points as wellas an improved contact efficiency between the chemical species.

Machines for synthesizing chemical chains or compounds onto a solidsubstrate have been in existence for many years. Typically suchsynthesizers make oligonucleotides by adding one phosphoramodite (base)at a time onto solid beads. The bases, A, T, C or G, are strung togetherinto a chain of the desired sequence and length. The process of addingthese bases may vary from manufacturer to manufacturer. The solidsubstrate is usually a batch of small polystyrene or glass beads(typically less than 1 mm diameter). A plurality of beads are placed ina container and fluids are passed through the beads. The process usuallycomprises adding these bases by the following process (1) detritylation,(2) applying base A, T, C or G, (3) adding an activator, (4) applyingcaping agent A and B, (5) washing with a first solvent, (6) applying anoxidizer, and (7) washing with a second solvent. This process adds onebase onto the beads and is repeated for each base desired. The onlyprocess variable is the base A, T, C or G which is determined by thecompound or chain desired. After all the desired bases are added, theoligos are cleaved (separated) from the beads by an ammonia solution. Anextraction process, such as High-pressure Liquid Cromotography (HPLC),separates and purifies the oligos from the ammonia. The final oligoproduct is in a liquid form that is often marked and stored before beingused or sold. The user, typically using a robot, must then conductanother set of steps to deposit and immobilize the liquid oligos onto asolid substrate for analysis purposes.

The disadvantage with existing synthesizers is that the final product isoften not application ready. The product is in a liquid form that musttypically be inventoried, stored, and usually reapplied onto anothersubstrate, such as a titer-plate or micro-slide, to be analyzed. A moreefficient process would be to synthesize the oligos on the samesubstrate that is ultimately analyzed. Furthermore, if the synthesisprocess could be automated such that the substrate is continuously fedthrough the solution, rather than the solution being fed through thesubstrate, the synthesized product could be placed directly onto theanalysis device without the need for inventory, storage, orre-application.

SUMMARY OF THE INVENTION

According to one aspect of the invention there is provided a fiber arrayfor contacting at least two chemical species. The fiber array comprisesa support plate having a channel for receiving a mobile chemical speciesand a fiber, having a second chemical species immobilized thereon,disposed on the support plate. At least a portion of the fiber isexposed to the channel such that the mobile chemical species is capableof contacting the second chemical species. More specifically, the fiberarray may be constructed as a matrix of multiple parallel fibersdisposed perpendicular to multiple parallel channels, thereby creating amatrix of contact points or mix points between each fiber and eachchannel.

The invention also provides a method for contacting at least twochemical species and for analyzing the contact between the at least twochemical species. The method for contacting the chemical speciescomprises immobilizing a chemical species on a fiber, placing the fiberon a support having a channel, and disposing a second, mobile chemicalspecies into the channel such that the mobile chemical species contactsthe fiber. The method for analyzing the contact between the two chemicalspecies, comprises immobilizing an immobilized chemical species on atleast a first one of a plurality of optical fibers, placing theplurality of fibers on a support having a plurality of channels,disposing a mobile chemical species into at least a first one of theplurality of channels such that the mobile chemical species contacts atleast the first one of a plurality of optical fibers, directing lightinto an end of the at least first one of a plurality of optical fibers,and viewing the excitation light emitted from the surface of at leastfirst one of a plurality of optical fibers. It should be appreciatedthat the excitation light is that light emitted from the fiber and mayalso be referred to below as binding light that is produced asindicative of an interaction between two chemical species.

The invention also provides a method for making a microchip having aplurality of contact points, comprising immobilizing each of a pluralityof known chemical species on a separate fiber and placing each of thefibers on a support having a plurality of parallel and fluidlyindependent channels for receiving an analyte, wherein the plurality offibers are arranged in parallel on the support and substantially normalto the plurality of channels, thereby forming a matrix of contactpositions between a portion of each of the fibers and each of theplurality of channels, such that each of the fibers is contacted by theanalyte.

The invention also provides an apparatus for detecting the binding ofthe two chemical species. The apparatus comprises a photo-detector forreceiving excitation light emitted from a mobile chemical species boundto an immobilized chemical species on a fiber. The apparatus alsocomprises a light source, a focusing lens for directing the light to anend of the fiber, and an electrical measuring device electricallyconnected to the photo-detector.

According to the invention there is furthermore provided a method fordetecting the binding of two chemical species, comprising the steps ofdirecting light to a fiber having an immobilized chemical species thathas been contacted with a mobile chemical species, and detectingexcitation light emitted from the chemical species bound to theimmobilized chemical species.

In another aspect of the invention, a fiber wheel mixing apparatus isprovided for contacting at least two chemical species. The fiber wheelmixing apparatus comprises a wheel having a perimeter sidewall, at leastone fiber disposed on the perimeter sidewall, and an immobilizedchemical species disposed on the fiber. Methods for making the fiberwheel mixing apparatus and for using the fiber wheel mixing apparatusare also provided.

The fiber wheel mixing apparatus of the present invention presents alow-cost method for contacting two or more chemical species. Each wheelcan include hundreds to thousands of fiber segments providing hundredsto thousands of mix points. By preparing and storing such wheels inadvance, a customized fiber wheel mixing apparatus can be rapidlyprepared to provide hundreds of thousands to a million mix points ormore. This type of mass contacting apparatus provides a significantlyenhanced throughput over typical conventional spotting techniques. Thethroughput would also scale linearly with the length of the fiber andthe number of fibers disposed on each wheel. Furthermore, by employingmultiple wheels, multiple samples can be simultaneously mixed andtested. Because the processing time for multiple samples is not muchgreater than that for processing a single sample, labor cost per samplecan also be reduced.

According to the invention there is further provided an apparatus forsynthesizing a chemical compound on a fiber, comprising at least onedepositor capable of depositing a chemical species precursor on a fiber,a transporter for bringing the fiber and the chemical species precursorinto proximity with one another such that the chemical species precursoris deposited on the fiber, and a selector for controlling the order inwhich each of a plurality of chemical species precursors is deposited onthe fiber, whereby a predetermined chemical species is synthesized onthe fiber.

Still further according to one aspect of the invention there is provideda method for synthesizing the chemical species on the fiber comprisingthe steps of determining an order for depositing a plurality of chemicalspecies precursors on a fiber, and depositing each of the precursors onthe fiber in the order to synthesize a predetermined chemical species.

Finally, according to the invention there is provided a method foranalyzing the contact between two chemical species comprising the stepsof synthesizing a predetermined chemical species on a fiber, contactingthe fiber with a mobile chemical species, passing light to the fiber,detecting excitation light emitted from the fiber.

The invention further provides a system for reading a microchip. Thesystem comprises a plurality of optical fibers each having apolynucleotide probe immobilized thereon and each having a first end.The system also includes a support for the plurality of fibers having aplurality of parallel and fluidly independent channels for receiving afirst analyte, wherein the plurality of fibers are arranged in parallelon the support and substantially normal to the plurality of channels,thereby forming a matrix of contact positions between each of the fibersand each of the plurality of channels, such that each of the fibers iscontacted by the first analyte. The system further comprises a lightsource for generating light, a focusing lens for focusing the light onan end of each of the fibers, a light detecting device positioned toreceive the excitation light emitted from each of the contact positions,and a motion device connected to the support to align each of the endswith the light.

Other features and advantages of the invention will appear from thefollowing description from which the preferred embodiments are set forthin detail in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a top plan view of a fiber array according to the presentinvention;

FIG. 2 is a cross-sectional view along line 2—2 of the fiber array ofFIG. 1 according to the present invention;

FIG. 3 is a cross-sectional view along line 3—3 of the fiber array ofFIG. 1 according to the present invention;

FIG. 4 is a top plan view of another embodiment of a fiber arrayaccording to the present invention;

FIG. 5 is a cross-sectional view along line 5—5 of the fiber array ofFIG. 4 according to the present invention;

FIG. 6 is a cross-sectional view of another embodiment of the fiberarray 10A of FIG. 4;

FIG. 7 is a cross-sectional view along line 6—6 of the fiber array ofFIG. 4 according to the present invention;

FIG. 8 is a top plan view of a device for moving the fluid through thechannels of a fiber array according to the present invention;

FIG. 9 is a top plan view of another embodiment of a fiber arrayaccording to the present invention;

FIG. 10 is a cross-sectional view of a fluid dispensing device for use athe fiber array according to the present invention;

FIG. 11 is a perspective view of a portion of another embodiment of afiber array according to the present invention;

FIG. 11A is a perspective view of a portion of yet another embodiment ofa fiber array according to the present invention;

FIG. 12 is a schematic of an embodiment of a fiber array readeraccording to the present invention;

FIG. 13 is a schematic of the interface between the light source and thefiber shown in FIG. 11;

FIG. 14 is a perspective view of an embodiment of a plurality ofchannels used in a fiber array according to the present invention;

FIG. 15 is an end view of another embodiment of a plurality of channelsused in a fiber array according to the present invention;

FIG. 16 is an side view of the embodiment shown in FIG. 14;

FIG. 17 is another embodiment of a fiber array reader according to thepresent invention;

FIG. 18 is yet another embodiment of a fiber array reader according tothe present invention;

FIG. 19 is another embodiment of a fiber array according to the presentinvention;

FIG. 20 is a perspective view of a wheel according to one embodiment ofthe present invention;

FIG. 21 is a perspective view of a cylinder according to one embodimentof the present invention;

FIG. 22 is a cross-sectional view of a wheel coupled to a wheel rotationdevice according to one embodiment of the present invention;

FIG. 23 is a cross-sectional view of a container coupled to a containerrotation device according to one embodiment of the present invention;

FIG. 24 is a cross-sectional view of a fluid delivery system accordingto one embodiment of the present invention;

FIG. 25 is a cross-sectional view of a fiber wheel mixing systemaccording to one embodiment of the present invention;

FIG. 26 is a top plan view of the fiber wheel mixing system of FIG. 25;

FIG. 27 is a light evaluating system according to one embodiment of thepresent invention;

FIG. 28 is another embodiment of the light evaluating system of FIG. 27;

FIG. 29 is yet another embodiment of a light evaluating system accordingto the present invention;

FIG. 30 is a cross-sectional view of another embodiment of a fiber wheelmixing system including a wheel assembly and a multi-cavity containeraccording to the present invention;

FIG. 31 is another cross-sectional view of the fiber wheel mixing systemof FIG. 30;

FIG. 32 shows one embodiment for preparing a fiber for use in a fiberarray according to the present invention;

FIG. 33 shows another embodiment for preparing a fiber for use in thefiber array according to the present invention;

FIG. 34 is a diagrammatic view of the invention;

FIGS. 35A, 35B and 35C is a side view of one embodiment of theinvention;

FIGS. 36A, 36B and 36C is a side view of another embodiment of theinvention;

FIGS. 37A, 37B and 37C is of yet another embodiment of the invention;

FIG. 38 is a perspective view of a preferred embodiment of theinvention;

FIG. 39 is an enlarged perspective view of the fiber cutting deviceillustrated in FIG. 38;

FIG. 40 is a side view of the coating module illustrated in FIG. 38;

FIG. 41 is a side view of the stacked coating modules illustrated inFIG. 38;

FIG. 42 is an enlarged side view of the deprotection module illustratedin FIG. 38;

FIG. 43 is an enlarged side view of another embodiment of a coatingmodule according to the present invention; and

FIG. 44 is a perspective view of the embodiment of the inventionillustrated in FIG. 43.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The fiber array of the present invention provides a simple and reliablesystem for contacting at least two chemical species. Through the use offibers, the fiber arrays of the invention provide myriad advantages overcurrently available micro-arrays. For example, fibers having one or aplurality of chemical species immobilized thereon can be prepared inadvance and stored, thereby permitting rapid assembly of customizedarrays. Quite significantly, customized arrays comprising differenttypes of chemical species can be prepared as conveniently and rapidly asarrays comprised of a single type of chemical species.

Moreover, the arrays of the invention provide reliability that ispresently unattainable in the art. For the conventional described above,verifying the integrity of the array prior to use is virtuallyimpossible—chemical species immobilized at each spot in the array wouldhave to be individually analyzed—a task which would be quite laborintensive and, given the small quantities of chemical speciesimmobilized at a spot, may even be impossible. In the arrays of theinstant invention, the integrity of the chemical species immobilized ona fiber can be determined by simply analyzing a small portion of theentire fiber. Thus, through the use of fibers, the invention provides,for the first time, the ability to construct arrays of from a few to asmany as thousands, millions, or even billions of immobilized compoundsrapidly, reproducibly, and with a degree of fidelity that isunprecedented in the art.

In addition, because the chemistry for fabricating an array can beperformed in advance, the fiber array of the present invention alsoavoids wicking, cleaning, and on-line loading associated withimmobilizing the chemical with current deposition methods.

Construction of the fiber array is relatively simple. The placement ofthe fiber on the array is generally only sensitive in one direction,since each fiber can be placed anywhere along its axis. Spotting amicro-array, however, requires the handling of thousands of drops whichhave to be placed in very specific locations defined by two dimensions.Furthermore, spotting may result in contamination between contactpoints, whereas, fibers, each having different chemical speciesimmobilized thereon, may be placed next to each other with a reducedpotential for such contamination. In situ methods require thedevelopment of specialized chemistries and/or masking strategies. Incontrast, the arrays of the present invention do not suffer from thesedrawbacks. They can take advantage of well-known chemistries, and do notrequire deposition of precise volumes of liquids at definedxy-coordinates. The size of the fiber array of the present inventionalso allows for a large number of contact points with a relatively smallarray, thereby reducing the costs of making the array. The fiber arrayof the present invention also provides for a large number of contactpoints without the need for significant duplication.

Use of the fiber array of the present invention allows the firstchemical to be easily dispensed into channels in the array in order tocontact the fibers. In addition, different chemical species may bedispensed into each of the channels, which allows each contact point tobe unique. Further, preferred fiber arrays of the present inventionprovide for a relatively high signal to noise ratio, since the use offibers with optical properties allows for more controlled illuminationof the contact points. The fiber array of the present invention isparticularly suited for use in performing nucleic array by hybridizationassays for applications such as sequencing by hybridization anddetecting polymorphisms among others.

FIGS. 1-3 are various views of one embodiment of a fiber array accordingto the present invention. FIG. 1 is a top plan view of a fiber array 100comprising a support plate 102, a pair of end walls 104, 202 and aplurality of channel walls 106 which extend from one end of the supportplate 102 to the opposite end. The channel walls 106 form a plurality ofchannels 108, which also extend from one end of the support plate 102 tothe opposite end, for receiving a fluid containing a chemical species ofinterest. Preferably, the channel walls 106 and the channels 108 areessentially parallel.

The fiber array 100 further comprises a plurality of fibers 110 eachhaving immobilized thereon a chemical species of interest to becontacted with the chemical species dispensed in the channels 108. Thefibers 110 are disposed on the plurality of channel walls 106 such thateach fiber 110 is physically separated from each adjacent fiber 110.Preferably, the fibers 110 are placed in a position essentially parallelto each other and essentially normal to the channels such that a portionof each fiber 110 is in fluid contact with the fluid in each channel108. This arrangement of the fibers 110 relative to the channels 108effectively creates a matrix or array of contact points 112 or mixpoints between the chemical species in the fluid in each of the channels108 and the chemical species immobilized on each fiber 110.

FIG. 2 is a cross-sectional view along line 2—2 of FIG. 1 of the fiberarray 100 according to the present invention. The channel walls 106 aredesigned to receive the fibers 110. As shown, the channel walls 106 havea groove 200 on top of the channel walls 106 to receive the fibers 110.This allows the fibers 110 to extend into the channels 108 to providefor direct contact between at least a bottom portion of each of thefibers 110 and the fluid in the channels 108. One of skill in the artwould recognize that a different geometry for the groove 200 can be usedbased upon the geometry of the fibers 110.

FIG. 3 is a cross-sectional view along line 3—3 of FIG. 1 of the fiberarray 100 according to the present invention. The channels 108 areformed by the channel walls 106 and the top of the support plate 102 andextend along the support plate 102 until terminated by end walls 104,202. Again, a bottom portion of each fiber 110 is exposed to eachchannel 108 such that placing a fluid in channel 108 will result incontact between the chemical species in the fluid and the chemicalspecies immobilized on each of the fibers 110.

The support plate 102, end walls 104, 202 and channel walls 106 may bemade of any material that is essentially inert to the chemical speciesof interest. One of ordinary skill in the art would be able to select anappropriate material for these features. In one embodiment the supportplate 102, end walls 104, 202 and channel walls 106 may be made of ahydrophobic material to reduce seepage of fluid through the channelwalls 106, thereby wetting only the fibers 110 and reducing the amountof fluid required. It should be appreciated that the dimensions of thesupport plate 102, end walls 104, 202 and channel walls 106, includingthe number of channels 108, may be altered depending upon the size ofthe array desired and the amount of fluid available to dispense in thechannels 108. However, it is important to keep the height of the channelwalls 106, the grooves 200, and the distance between the channel walls106 of such relative proportions to insure sufficient exposure of thesurface area of the fibers 110 to the fluid in the channels 108.Further, it should be appreciated that the thickness of the channelwalls 106 may also be altered to optimize the overall size of the fiberarray 100. Without limiting the dimensions of an array that could bemade according to the present invention, typical dimensions for thesupport plate may range from 1cm to 1000 cm. The thickness of thechannel walls may range from 10 μm to 1000 μm, and the channel width mayrange from of 10 μm to 1000 μm. The height of the channel walls mayrange from 10 μm to 1000 μm.

The fiber 110 can be composed of virtually any material or mixture ofmaterials suitable for immobilizing the particular type of chemicalspecies. For example, as will be discussed in conjunction with FIG. 12,the fiber may be an electrically conductive wire. Alternatively, thefiber may be an optical fiber. Moreover, the use of the term “fiber” isnot intended to imply any limitation with respect to its composition ormaterials of construction or geometry. Preferably, the fiber 110 willnot melt, degrade, or otherwise deteriorate under the conditions used toimmobilize the chemical species or under the desired assay conditions.In addition, the fiber 110 should be composed of a material or mixtureof materials that does not readily release the immobilized chemicalspecies under the desired assay conditions. The actual choice ofmaterial will depend upon, among other factors, the identity of thechemical species immobilized and the mode of immobilization and will beapparent to those of skill in the art.

As will be discussed in more detail in conjunction with the preparationof the fiber 110, below, in embodiments employing covalent attachment ofthe chemical species, the fiber 110 is preferably composed of a materialor mixture of materials that can be readily activated or derivatizedwith reactive groups suitable for effecting covalent attachment.Non-limiting examples of suitable materials include acrylic,styrene-methyl methacrylate copolymers, ethylene/acrylic acid,acrylonitrile-butadiene-styrene (ABS), ABS/polycarbonate,ABS/polysulfone, ABS/polyvinyl chloride, ethylene propylene, ethylenevinyl acetate (EVA), nitrocellulose, nylons (including nylon 6, nylon6/6, nylon 6/6-6, nylon 6/9, nylon 6/10, nylon 6/12, nylon 11 and nylon12), polycarylonitrile (PAN), polyacrylate, polycarbonate, polybutyleneterephthalate (PBT), polyethylene terephthalate (PET), polyethylene(including low density, linear low density, high density, cross-linkedand ultra-high molecular weight grades), polypropylene homopolymer,polypropylene copolymers, polystyrene (including general purpose andhigh impact grades), polytetrafluoroethylene (PTFE), fluorinatedethylene-propylene (FEP), ethylene-tetrafluoroethylene (ETFE),perfluoroalkoxyethylene (PFA), polyvinyl fluoride (PVA), polyvinylidenefluoride (PVDF), polychlorotrifluoroethylene (PCTFE),polyethylene-chlorotrifluoroethylene (ECTFE), polyvinyl alcohol (PVA),silicon styrene-acrylonitrile (SAN), styrene maleic anhydride (SMA),metal oxides, and glass.

In a preferred embodiment, the fiber 110 is an optical fiber. Theoptical fiber is typically between about 10 μm and 1000 μm in diameterand can be comprised of virtually any material so long as it is anoptical conductor at the wave length of interest. For example, theoptical fiber may be an organic material such as polymethacrylate,polystyrene, polymethyl phenyl siloxane, or deuterated methylmethacrylate, or it may be an inorganic material such as glass. Incertain embodiments of the invention, a beam of light directed throughsuch optical fiber can be used to detect and/or quantify the interactionbetween the chemical species in the fluid and the chemical species onthe fibers (described below).

It should be appreciated that each fiber 110 may actually contain adifferent chemical species, or multiple chemical species, in differentpositions along the fiber 110 or in multiple layers on the fiber 110.Therefore, the preparation of each fiber 110 and immobilization of thedesired chemical species thereto will vary depending upon the type offiber 110 used, the mode of immobilization, and the identity of thechemical species. Various methods for preparing fibers having a varietyof chemical species immobilized thereon are discussed in detail in alater section.

The number of fibers 110 comprising fiber array 100 will vary dependingupon the size of the matrix desired or the number of different chemicalspecies desired to be reacted with the chemical species in the channels108. The fibers 110 may be almost any length; however, the length shouldpreferably be sufficient to traverse all of the channels 108. It shouldbe appreciated, however, that the fibers 110 may actually be of anylength, diameter, or shape.

In general operation and use of the fiber array 100, a fluid containingone chemical species of interest is dispensed into the channels 108. Thefluid may be dispensed using any method known in the art for dispensinga fluid, such as pumping, aspirating, gravity flow, electrical pulsing,vacuum or suction, capillary action, or electro-osmosis. (One device fordispensing fluid onto the fiber array 100 is described below inconnection with FIG. 10.) Enough fluid is dispensed to insure contactwith a portion of some or all of the fibers 110. The fiber is contactedwith the fluid under conditions and for a period of time conducive topromoting interaction between the two chemical species. In instanceswhere excess chemical species in the fluid interferes with the detectionof the interaction, the fluid may be removed and the fibers optionallywashed prior to detection. The interaction, if any, between the chemicalspecies in the fluid and that on the fibers 110 is then analyzed at oneor more contact points 112.

In some instances such as assays involving hybridization of nucleicacids, it may be desirable to control the temperature of the fiber arrayduring the assay. This can be achieved using a variety of conventionalmeans. For example, if the device is constructed of an appropriateconductor, such as anodized aluminum, the device may be contacted withan appropriately controlled external heat source. In this instance, thefiber array would act essentially as a heat block. Alternatively, thechannels 108 could be outfitted with heaters and thermocouples tocontrol the temperature of the fluid disposed within the channels.

The method by which the interaction is analyzed will depend upon theparticular array. For example, where the two chemical species eachconstitute one member of a binding pair of molecules ( for example, aligand and its receptor or two complementary polynucleotides), theinteraction can be conveniently analyzed by labeling one member of thepair, typically the chemical species in solution, with a moiety thatproduces a detectable signal upon binding. Only those contact points 112where binding has taken place will produce a detectable signal.

Any label capable of producing a detectable signal can be used. Suchlabels include, but are not limited to, radioisotopes, chromophores,fluorophores, lumophores, chemiluminescent moieties, etc. The label mayalso be a compound capable of producing a detectable signal, such as anenzyme capable of catalyzing, e.g., a light-emitting reaction or acalorimetric reaction. Preferably, the label is a moiety capable ofabsorbing or emitting light, such as a chromophore or a fluorophore.

Alternatively, both chemical species are unlabeled and their interactionis indirectly analyzed with a reporter moiety that specifically detectsthe interaction. For example, binding between an immobilized antigen anda first antibody (or visa versa) could be analyzed with a labeled secondantibody specific for the antigen-first antibody complex. Forpolynucleic acids, the presence of hybrids could be detected byintercalating dyes, such as ethidium bromide, which are specific fordouble-stranded nucleic acids.

Those of skill in the art will recognize that the above-described modesof detecting an interaction between the two chemical species at acontact point are merely illustrative. Other methods of detecting myriadtypes of interactions between chemical species are well known in the artand can be readily used or adapted for use with the fiber arrays of thepresent invention.

It should be appreciated that since each channel 108 is fluidly isolatedfrom each other channel 108, a different chemical species may bedispensed into each channel 108. If each fiber 110 has a differentchemical species immobilized thereon, this would create a matrix ofcontact points 112 in which each contact point 112 is unique.Furthermore, while not a preferred mode of operation, chemical speciesmay be serially or simultaneously dispensed into the same channels 108.Sequential dispersing is particularly useful, for example, where thechemical species immobilized on fiber 110 is synthesized in situ on thefiber 110.

FIGS. 4-6 are various views of another embodiment of a fiber array 400according to the present invention. Fiber array 400 is similar to fiberarray 100, but with the addition of a cover plate 402. FIGS. 4-6 areessentially the same views as FIGS. 1-3, but show a cover plate 402. Itshould be appreciated that while a cover plate is convenient inoperation and use of the fiber array, it is not necessary.

FIG. 4 is a top plan view of fiber array 400, according the presentinvention. Cover plate 402 comprises a plurality of channel inlet ports404, which are each fluidly connected to separate channels 108 at oneend of the channels 108, and a plurality of channel outlet ports 406,which are also each fluidly connected to separate channels 108 at theopposite end of the channels 108. The channel inlet ports 404 provide anopening through which the fluid containing a chemical species ofinterest is dispensed into a respective channel 108. The channel outletports 406 allow the fluid to exit the fiber array 400. Similar to thesupport plate 102, cover plate 402 may be made of any material that isessentially inert to the chemical species of interest, and one ofordinary skill in the art would be able to select an appropriatematerial. Further, it should be appreciated that cover plate 402 may betransparent to facilitate detection of the interaction between thechemical species being contacted.

FIG. 5 is a cross-sectional view of the fiber array 400 along line 5—5of FIG. 4. The cover plate 402 comprises a pair of end walls 504, 506which mate with the end walls 104, 202, respectively, of the supportplate 102. The cover plate 402 further comprises a plurality of channelwalls 508 which also mate with the channel walls 106 to seal eachchannel 108 such that fluid cannot pass from one channel to another. Thechannel walls 508 also have grooves 510 for receiving the fibers 110.The channel walls 508 and the channel walls 106 also mate to enclose andsecure those portions of the fibers 110 laying within the grooves 510,200. It should be appreciated that the cover plate 402 may be secured tothe support plate 102 by any method for adhering two materials dependingupon their specific composition. For example, diffusion bonding, inertadhesives, laser or ultrasonic welding, or fasteners may all be used.Other methods for securing two structures together are well known in theart.

FIG. 6 is a cross-sectional view of the fiber array 400 along line 6—6of FIG. 4. The channels 108 extend above and below the fibers 110 suchthat the longitudinal portions of the fibers 110 exposed to the channels108 may be surrounded by the fluid introduced into the channels 108. Thechannel outlet ports 46 extend through the cover plate 42 to allow thefluid to pass from the channels 108 through the cover plate 42 and outof the fiber array 400. The channel inlet ports are constructed in asimilar fashion to allow the fluid to pass through the cover plate 42into the channels 108.

The operation and use of the fiber array 400 with the cover plate 402 isessentially the same as the fiber array 100 without the cover plate 402.However, the cover plate 402 fluidly seals each of the channels 108,thereby allowing for other methods to be used to move the fluid throughthe channels 108. For example, a pump may be used to pressurize thefluid in the channels 108, thereby forcing the fluid through thechannels. Alternatively, centrifugal force may be used to force thefluid through the channels.

FIG. 7 is a cross-sectional view of another embodiment of the fiberarray 400 of FIG. 4 illustrating a preferred design for securing thefibers 110 between the support plate and the cover plate. As shown,support plate 700 comprises grooves 702 for receiving the fibers 110.Cover plate 704 comprises a plurality of teeth 706 which correspond andmate with the grooves 702. This configuration allows the cover plate tobe more easily aligned in securing it to the support plate 700, sinceany tooth 706 may be mated with any groove 702. It should be appreciatedthat any design or shape for the teeth and the groove may be used.Moreover, it should be appreciated that the fiber array 400 may beconstructed without grooves for securing the fibers 110, and the fibersmay simply be pinched between the support plate and the cover plate uponsecuring the support plate to the cover plate.

FIG. 8 is a top plan view of a device for moving the fluid through thechannels 108 of the fiber array 400 having a cover plate 402. Rotatingplate 800 is any device which can be rotated about its center axis. Thefiber array 400 is secured to the rotating plate 800 such that thechannel inlet ports 404 are located near the center of the rotatingplate 800, and the channels 108 extend radially outward toward the outerperimeter of the rotating plate 800. The fiber array 400 may be securedto the rotating plate 800 by any means known in the art such as hooks,clips, screws, bolts, magnets and the like. As the rotating plate 800 isrotated about its axis, centrifugal force will move the fluid from theend of the channels 108 near the channel inlet ports 404 through thechannels 108 toward the channel outlet ports 406, thereby moving thefluid past each fiber 110. The channel outlet ports 406 may be sealed toprevent the fluid from exiting the fiber array during rotation. Itshould be recognized that additional fiber arrays may be placed on therotating plate 800 at the same time.

FIG. 9 is a top plan view of another embodiment of a fiber array 900according to the present invention. The fiber array 900 is similar tothe fiber array described in connection with FIGS. 1-8, comprising aplurality of fibers 110 and a plurality of channels 902 intersecting thefibers 110. Preferably, the fibers 110 are essentially parallel to eachother, and the channels 902 are essentially perpendicular to the fibers110. The fiber array 900, however, additionally comprises a plurality ofchannel inlet ports 904 which are each connected to a respective channelinlet line 906. Each channel inlet line 906 is connected to one end of arespective channel 902 and allows fluid to pass from each of the channelinlet ports 904 to its respective channel 902 within the fiber array900. The opposite end of each channel 902 is sealed.

The channel inlet ports 904 are arranged to facilitate dispensing thefluid into each channel inlet port 904 with ease and without resort totechniques and micro-sized equipment for dispensing fluid into extremelysmall openings. With a larger opening, each channel inlet port 904 canaccommodate a larger apparatus for dispensing fluid such as a pipette orsyringe, thereby reducing the error associated with the transfer ofsmall volumes of fluid.

To provide such larger openings, the channel inlet ports 904 arepositioned adjacent to the fiber array 900 and are connected to theirrespective channels 902 by a channel inlet line 906. FIG. 9 showsseveral groups of ten channel inlet ports 904, each arranged onalternating sides of the fiber array 900. Each channel inlet port 904within one group is offset in two directions from its adjacent channelinlet port 904. Specifically, each channel inlet port 904 is offset in adirection parallel to the channels by a distance equivalent to the sizeof the opening of the channel inlet port 904 and in a direction parallelto the fibers 110 by a distance equivalent to one channel width. Thisnecessitates that each channel inlet line 906 will be of increasinglength. However, in this manner the size of the channel inlet port 904can be maintained, as well as the alignment between the channel inletport 904, its respective channel inlet line 906 and its respectivechannel 902.

The channel inlet ports 904 are arranged in this fashion until the widthof all of the adjacent channel inlet ports 904 in one group, as measuredin a direction parallel to the fibers, is equivalent to the size of theopening of one channel inlet port 904. This arrangement of a group ofchannel inlet ports 904 is then repeated on the opposite side of thefiber array 900. This alternating arrangement of groups of channel inletports 904 and their respective channel inlet lines 906 can be continuedalong the fiber array 900 indefinitely. While this is the preferredarrangement of the channel inlet ports 904 and their respective channelinlet lines 906, it should be appreciated that the channel inlet ports904 may actually be positioned in any fashion along the fiber array 900.

It should be noted that the channels 902 are also positioned in analternating fashion corresponding to the groups of channel inlet lines906, since one end of each channel 902 is sealed. Therefore, inalternating fashion, a number of channels 902, equivalent to the numberof channel inlet lines 906, will have their open ends on one side of thefiber array 900 and the next group of channels 902 will have their openends on the other side of the fiber array 900. Further, since thechannels 902 are sealed at one end there is no channel outlet port.Therefore, in operation, a sufficient quantity of fluid is simplydispensed into the channel inlet ports 904 and is not removed from thechannels 902.

FIG. 10 is a cross-sectional view of a fluid dispensing device for usewith the fiber array 100 of FIGS. 1-3. The fluid dispensing device 1000comprises a fluid dispenser body 1002 which fixedly holds a plurality offluid dispensers 1004, each having a fluid dispenser opening 1006. Eachfluid dispenser 84 is aligned over a channel 108 such that there is onefluid dispenser 1004 for each channel 108. It should be appreciated,however, that a greater or lesser number of fluid dispensers 1004 may beused to feed additional channels or to provide more than one dispenserper channel. Fluid is fed to each fluid dispenser opening 1006 by afluid feed line 1008 which is fluidly connected to a fluid deliverysystem 1010. The fluid delivery system. 1010 may be any system known inthe art that is capable of metering and delivering fluid to a fluidline, such as a pump, an aspirator, by capillary action, by moving agiven quantity of fluid from a reservoir through the fluid feed lines1008 and out of the fluid dispenser openings 1006. The fluid dispenseropenings 1006 permit the fluid to be disposed either into the channels108 or onto the fibers 110. The dispenser openings 1006 may be simplyopenings at the end of the fluid feed line 1008, nozzles, pipette tips,syringe or needle tips, capillary tubes, quills, or ink jets. Otherdevices through which a fluid is conveyed are well known in the art. Itshould be appreciated that the fluid delivery system 1010 should alsohave the capability of metering and delivering different fluids to eachof the fluid feed lines 1008. This permits the ability to contact eachof the fibers with a different chemical species.

The fluid dispenser body 1002 is connected to a motion device 1012 whichacts to move the fluid dispenser body 1002 in a direction parallel tothe channels 108. This permits the fluid dispensing device 1000 todispense fluid at various locations along each channel 108 or onto eachfiber 110. In addition, the motion device 1012 may move the fluiddispenser body 1002 in a direction parallel to the fibers. This allowsfor the use of fewer fluid dispensers 1004, since a given set of fluiddispensers 1004 may be moved and aligned to dispense fluid into anotherset of corresponding channels 108. The motion device 1012 may be anytype of mechanical device which operates to move an object within ahorizontal plane, such as a conveyor or a rotating screw system tocertain xy-coordinates. Motion devices of this type are well known inthe art.

In operation, a chemical species to be contacted with the chemicalspecies immobilized on the fibers 110 may be placed in a carrier fluidheld in a reservoir within the fluid delivery system 1010. Upon demand,for example by computer control, the fluid dispenser body 1002 is movedto a desired location above the fiber array 100, and the fluid deliverysystem 1010 delivers the fluid to the fluid dispensers 1004 andultimately to the respective channels 108 or onto the respective fibers110. Depending upon the geometry of the fiber array and the volume ofthe channels 108, the amount of fluid dispensed will vary; however, asufficient amount of fluid should be dispensed to insure adequatecontact with the fibers 110. The fluid dispenser body 1002 can then bemoved to another location, either along the same channel 108 or to adifferent channel 108 to dispense additional fluid. It should beappreciated that each fluid dispenser 1004 may dispense a differentfluid, or a second fluid may be dispensed after the first fluid isdispensed. In this latter case, rinsing of the fluid feed lines 1008 andthe fluid dispensers 1004 before dispensing the second fluid may beappropriate.

FIG. 11 is a perspective view of a portion of another embodiment of afiber array according to the present invention which useselectro-osmosis to move a fluid through the channels of the fiber arrayto assist in contacting the fluid and the fibers. The fiber array 1100is essentially the same as those previously described; however, thefibers 1110 are conductive. The fibers 1110 may be made conductive byapplying a conductive coating (not shown), which underlies the chemicalspecies (not shown) immobilized on the fibers 1110, such as silver orgold. Alternatively, the fibers 1110 may be made conductive byconstructing the fiber 1110 itself of a materially that is electricallyconductive and which optionally transmits light, such as indium tinoxide. A conductive contact 1116 surrounds the fibers 1110 at the edgeof the support plate 1118. The conductive contact 1116 serves as a meansfor electrically connecting a power supply 1124 to each of the fibers1110 using wires 1122. Wires 1126 connect the power supply 1124 to thefluid in channels 1120 thereby completing the circuit.

In operation, the fibers 1110 would be charged and made electricallyconductive by supplying power from the power supply 1124 to theconductive contact 1116 of each fiber 1110, and therefore, to theconductive coating of each fiber 1110. The fluid dispensed into thechannels 1120 would comprise, in addition to the chemical species ofinterest, an electrolyte that would be in contact with the power supply1124 using wires 1126, thereby completing the circuit. The applicationof power to the fibers 1110 causes the fluid containing the chemicalspecies of interest to move through the channel 1120 throughelectro-osmosis. Power may then be supplied to an adjacent fiber to movethe fluid further along the channel 1120. It should be appreciated thatpower may be supplied sequentially to single fibers or to groups offibers. It should also be appreciated that the voltage necessary forelectro-osmosis may vary with the electrolyte used, the chemical speciesof interest and the materials used to construct the channel walls, whichpreferably should be non-conductive, such as glass or plastic. Typicalvoltages applied to the fibers may range from a few volts to severalkilovolts. Therefore, power supply 1124 must be capable of providingsuch a range of voltages.

Additionally, electrophoretic forces may be used to provide a greaterdegree of contact between the chemical species of interest in the fluidand those immobilized on the fiber. Using the embodiment of FIG. 11, thepolarity of the fiber and the electrolytic fluid may be reversed usingthe power supply 1124 in an oscillating fashion at frequencies in thekilohertz range. By reversing the polarity in an alternating fashion,the chemical species of interest in the fluid may be drawn closer to thechemical species on the fiber and then pushed away in the event that thedesired interaction does not occur. The process of drawing the chemicalspecies in the fluid close to the fiber may increase the efficiency ofcontact between the chemical species. The process of pushing thechemical species in the fluid away from the fiber may increase theaccuracy of the interactions by reducing the number of falseinteractions wherein an interaction is detected due to non-specificbinding to the fiber, but not a true interaction between the chemicalspecies of interest. The voltages and oscillating frequencies necessaryto accomplish this will be dependent upon the composition of the fluidand the chemical species of interest. It should be appreciated, however,that the force used to push the chemical species in the fluid away fromthe fiber must not be so great as to disrupt a true interaction with thechemical species on the fiber. The use of electrophoresis is furtherdescribed in U.S. Pat. Nos. 5,605,662 and 5,632,957, both of which areincorporated herein by reference.

FIG. 11A is a perspective view of a portion of yet another embodiment ofa fiber array according to the present invention. In this embodiment,the wires 1122 may be positioned within the fluid at the end of thechannel distal from the end where wires 1126 are positioned. Both setsof wires 1122 and 1126 are connected to the power supply 1124, therebycompleting the circuit. In addition, it should be appreciated that theinvention may easily be adapted to provide a charged surface, using, forexample, a channel wall, that enables electro-osmosis orelectrophoresis.

As described above, the fiber array of the present invention is used tocontact at least two chemical species and to detect and/or quantify aninteraction between these species. One of skill in the art would be ableto select an appropriate detection method for use with the fiber arrayof the present invention, such as those previously described. In somecases, especially those instances where the interaction between thechemical species in solution and that immobilized on the fiber cause adifference in the absorbance or emission of light, such as thoseinstances where the chemical species disposed within the channels 108are labeled with a fluorophore, it is desirable to measure the amountand/or wavelength of light emanated from each of the contact points 112as a result of the interaction between the chemical species in thechannels 108 and on the fibers 110 using a light evaluating device suchas the human eye, a camera, or spectrometer. To accomplish this, theentire support plate 102 may be illuminated; however, this may createundesirable background illumination and reduce the signal to noise ratioin the light evaluating device. Therefore, it may be desirable to moreselectively illuminate a portion of the fiber array, for example asingle fiber or a group of fibers for evaluation, thereby providinggreater distinction between contact points 112.

FIG. 12 is a schematic of an embodiment of a fiber array reader 1200according to the present invention. The fiber array 1202 may be the sameas the fiber array 100 shown in FIGS. 1-3, the fiber array 400 having acover plate 402 as in FIGS. 4-6, or the fiber array 900 as in FIG. 9;however, the fibers 110 are optical fibers. For purposes of the presentinvention, an optical fiber is any material used as a fiber which istransparent to a given wavelength or wavelengths of light. The fiberarray reader 1200 consists of a light source 1204, such as an excitationlaser or an arc lamp, which produces a beam of light having the desiredwavelength, which is directed to the end of a fiber 110. A motion device1206 is used to move the light source 1204 and the fiber array 1202,relative to one another. Either the light source 1204 is moved, thefiber array 1202 is moved, or both are moved relative to one another bythe motion device 1206. Any motion device 1206 known in the art may beused such as a stepper motor or a conveyor powered by a reversible motorcapable of moving the conveyor back and forth. A motion detection systemwith motion sensors (not shown), such as infrared light sensors, may beused to monitor the position of the motion device 1206. The reader 1200may further comprise light evaluating devices or detectors 1208 whichmay comprise any device capable of receiving and at least qualitativelyevaluating light such as the human eye, a camera (e.g., confocal or CCDcamera) or a spectrometer. The detectors 1208 are positioned abovecontact or mix points 112 which occur at the intersection of the fibers110 and the channels 108. The reader 1200 may also include a heater 1212to ramp temperature as will be discussed infra in relation to FIG. 17.

In operation, a fluid is inserted into input holes 1210 at one end of achannel 108. The fiber 110 is thereby contacted with the fluidcontaining a chemical species under conditions conducive to interactionbetween the chemical species immobilized on fiber 110 and the chemicalspecies in solution. Each channel may receive a different or similarfluid.

FIG. 13 is a schematic view of the interface between the light source1204 and the fiber 110 shown in FIG. 12 once the fluid containing achemical species has contacted the fiber 110. The light source 1204generates light rays 1300 that are focused by a lens 1302 into an end ofa given fiber 110 (or group of fibers) and that reflect internallyinside of the fiber 110. A preferred lens 1302 is a cylindrical lensthat forms the rays 1300 into a focal point 1304 at the end of the fiber110. The focal point 1304 may form a plane perpendicular to the fiber110 so that of the fiber 110 and the light source 1204 do not requireexact alignment. The light reflecting inside the fiber 110 creates anevanescent wave 1306 on the surface of the fiber 110 illuminating thefiber surface. In a DNA hybridization application, the fluid containingthe chemical species or sample fragment 1308 could be a DNA fragmentlabeled with a fluoraphore. A probe DNA fragment 1310 is attached to thefiber 110 as explained supra. If the structure of the sample fragment1308 matches the structure of the probe DNA fragment 1310, the samplefragment 1308 will hybridize with the probe DNA fragment 1310 and remainat the fiber surface. Since the evanescent wave 1306 only illuminatesnear the fiber surface, the sample fragment 1308 labeled with thefluoraphore will be illuminated and fluoresce if hybridized to a probeDNA fragment 1310, while mismatch DNA will not hybridize and therefore,not fluoresce, since it is not near the fiber surface. Thus,hybridization of the sample fragment 1308 to a particular probe DNAfragment 1310 is indicated by the presence of fluorescent light when asample fragment 1308 is injected into the channel 108 and exposed to thefibers 110. If the interaction between the sample fragment 1308 and theprobe DNA fragment 1310 causes an increase or decrease in the absorbanceof a particular wavelength of light, the area around a contact point 112will emit either a greater or lesser quantity of light as compared withcontacts point 112 where no interaction occurred. The intensity of thisevanescent wave 1306 exponentially dissipates with distance from thesurface of the fiber 110 and almost disappears beyond 300 nanometers.Therefore, only the fiber 110, and the chemical species on the fiber,probe DNA fragment 1310, receiving the beam of light 1300 areilluminated. The material around the fiber 110 is not illuminated. Thus,the signal to noise ratio received by the light evaluating device ordetector is improved. Because of their selective illumination, theoptical fiber arrays of the invention can be advantageously used withassays where the chemical species in solution is labeled with afluorophore without first having to remove the excess, unreacted labeledspecies. The labeled species only produce a detectable fluorescencesignal if they interact with the chemical species immobilized on opticalfiber 110; labeled species free in solution are not illuminated and donot fluoresce. Of course, where desired, the excess unlabeled chemicalspecies can be removed prior to detection.

It should be appreciated that the wavelength of light used forilluminating the fibers will depend upon the optical absorption band ofthe fluorescent molecule. In addition, the light evaluating device needsto be able to detect the excitation light.

Referring to FIGS. 12 and 13, after measuring the light at a givencontact point 112, or set of contact points along a given fiber 110, orset of fibers, the light evaluating device 1208 may be moved, manuallyor automatically, to the next contact point 112, or set of contactpoints along the same fiber 110, or next set of fibers. Alternatively,there may be a light evaluating device 1208 fixed at each contact point112. Once all of the contact points 112 along a given fiber, or set offibers, have been evaluated, the motion device 1206 may move the lightsource 1204 and the focusing lens 1302 to the next fiber 110, or set offibers, such that the beam of light 1300 is aligned appropriately withthe end of the next fiber 110, set of fibers. Alternatively the lightevaluating device 1108 may be fixed, and the array 1102 may be moved asdescribed supra. It should be appreciated, however, that any contactpoint 112, or set of contact points may be evaluated in any sequence andin any time interval. One advantage of selectively illuminating certainfibers or groups of fibers, compared to illuminating the entire plate,is a reduction in noise from fibers and contact points that are adjacentto those being evaluated by the light evaluating device 1208. Thisreduces the potential confusion as to which contact points 112 are beingobserved.

FIG. 14 shows a perspective view of an embodiment of a channel 108 usedin a fiber array in connection with the use of a light source toilluminate the fibers 110. As shown, the bottom of the channel 108 hasmultiple curves positioned beneath where each fiber 110 would lay. Inaddition, the channel 108 may have a reflective coating 1400. Thecurvature of the bottom of the channel 108 and the reflective coating1400 act to reflect the light back towards the light evaluating deviceto improve the strength of the light signal received from each contactpoint. The reflective coating 1400 may be made from any material thatreflects light, such as, for example, aluminum, gold and mixturesthereof. Furthermore, the reflective coating 1400 may be multi-layered.It should be appreciated that while only one channel 108 is shown, eachchannel 108 may be similarly designed.

FIG. 15 is an end view of another embodiment of the channels 108 shownin FIG. 14, and FIG. 16 is a side view of the embodiment shown in FIG.15. The amount of fluorescent light 1500 collected into the detectoroptic 1502 can be increased by designing the curve of the channels 108to reflect light in a preferred direction. A preferred detector optic1502 is a fiber optic with a much larger diameter than the fiber 110.The detector optic 1502 directs the collected light intoa-photo-detector 1504, producing an electrical signal that isproportional to amount of light 1500. The preferred photo-detector 1504is a solid-state diode or a photo multiplier tube. The channel curvingcan be in all dimensions, and the reflection efficiency may vary, butthe general intent is to redirect light into the detector optic 1502that would otherwise be lost into the channel substrate 1506.

FIG. 17 is another embodiment of a fiber array reader 1700. Anelectrical signal is sent from a photo-detector 1702 through a cable1704 to an analog to digital converter 1706 where a digital signal isgenerated for interpretation and plotting by a computer 1708. Forexample, the signal data 1722 could be plotted as intensity 1710 overtime 1712. The fiber array 1714 can be arranged in a circulararrangement as shown to allow for continuous reading of the fibers 110.A motor 1716 rotates a hub 1718, supporting the fiber array 1714, atsome specified rate, such as for example one revolution per second. Alaser 1720 is fixed such that the light from laser 1720 forms a focusedline at the fiber-end, as discussed supra. In other words, the fibers110 are sequentially rotated into the focused line of laser light.Because the laser line or plane is much narrower than the spacingbetween the fiber's 110 diameters, the fibers need not be accuratelyplaced along that line for the light to enter the fiber. Furthermore,the fibers need not be accurately aligned in the orthogonal dimensioneither, as the fibers 110 are guaranteed to rotate into a fixed line oflight.

A heater/cooler 1724 uniformly controls the temperature of the fiberarray 1714. The signal from each fiber 110 is analyzed each rotation ofthe hub 1718 and a plot for each fiber mix-point is generatedindependent of any other fiber. Furthermore, the temperature is rampedover a range guaranteed to pass though the optimum temperature forbinding of a mobile and an immobilized chemical species. The optimumtemperature for DNA hybridization is the optimum hybridizationtemperature for that particular probe, as each probe has a differentoptimum hybridization temperature. Thus, each probe is observed at itsoptimum hybridization even though each probe in the fiber array 1714 hasa different optimum hybridization temperature.

FIG. 18 shows yet another embodiment of a fiber array reader 1800. Inthe case of very long fiber arrays 1814, the fiber array 1814 can berolled into a format similar to a typical audio-cassette tape. In thisconfiguration, one or more motors (not shown) move the array off one hub1818 and onto another hub 1820 with each fiber 110 passing under a fixeddetector optic 1826. Heater/cooler units 1824 may be provided in bothhubs 1818 and 1820. A laser 1870 is also provided. An ultrasonic mixingdevice 1804, preferably fixed in space, may be added to improve mixingof the fluids.

FIG. 19 is still another embodiment of a fiber array according to thepresent invention. The fiber array 1900 comprises a circular supportplate 1902 with the fibers 110 radially disposed on the support plate1902 such that one end of each fiber 110 is near the center of thesupport plate 1902 and the other end of the fiber 110 is near the outerperimeter of the support plate 1902. The fiber array 1900 also comprisesa plurality of channels 1904 in the support plate 1902. Although thechannels 1904 may be arranged in any fashion or pattern on the supportplate 1902, preferably, the channels 1904 are arranged in concentriccircles; however, it should be appreciated that it is not necessary tohave a channel which traverses an entire concentric circle. For example,a channel 1904 may simply be the length of a portion of a concentriccircle or an arc. The light source 1906 and focusing lens 1908 act toproject and direct the beam of light 1910 to the end of each of thefibers 110. In this embodiment, rather than move the light source 1906and the focusing lens 1908 to align the beam of light 1910 with eachfiber 110, the support plate 1902 is rotated such that each fiber 110 isaligned with the beam of light 1910. Again, a motion detection system(not shown) having motion sensors may be used to monitor the exactpositioning of the support plate 1902 to provide exact alignment withthe beam of light 1910. A cover 1912 may also be provided.

No image is necessary for the various readers, so a single diode maycollect the information. The signal from this diode can be quicklyconverted from analog to digital and recorded, reducing the amount ofdata as compared to a camera system. Since the detection system issimple and inexpensive, it is feasible to detect many channelssimultaneously, greatly increasing the throughput.

Furthermore, because the evanescence wave does not travel far beyond thefiber surface, the sample can remain in the channel duringhybridization, avoiding washing and allowing real-time reading. Thus,the fluorescent signal can be monitored while temperature is ramped.Rather than a snap-shot information, information on hybridization overtime is collected, providing much higher specificity and real timemonitoring.

The fiber arrays may contain 100,000 or more fibers that could bequickly detected by these readers and many channels may be readsimultaneously, resulting in a high density of information.

The light-source may also directly illuminate the mix points through thefiber to reduce stray light and unwanted reflections. Thus, reducing thenoise level. In a desirable contrast, the signal level is higher becausethe cylindrical shape of the fiber focuses fluorescence rays passingthrough it. This focusing results in the collection of fluorescence raysthat otherwise would be lost.

Furthermore, only the fibers are illuminated, avoiding the wastefulprocess of flood illuminating the entire surface area, and thus,reducing the amount of illumination power needed.

Any of the above reader embodiments may include an adaptive filter tofilter out common noise such as reflecting light. To calibrate thesystem all detectors are activated when no chemical species is present.All detectors are then set to zero using mathematical manipulation suchas a transfer function. The chemical species is then added to thesystem. Any change in signal from the detectors is therefore caused bythe added chemicals species.

In yet another aspect of the invention, the fibers 110, which have beendescribed above, are incorporated into a fiber wheel mixing system forcontacting at least two chemical species. It should be appreciated thatthe fiber wheel mixing system may be used for any of the chemicalinteractions described previously in connection with the fiber array.The fiber wheel mixing system generally includes a container forreceiving a mobile chemical species and a wheel including fibers havinga chemical species immobilized thereon. FIGS. 20 through 26 and 30 and31 show various embodiments of the fiber wheel mixing system. FIGS. 27to 29 show various embodiments of a light evaluating system fordetecting and evaluating light signals generated as a result of mixingbetween two chemical species.

FIG. 20 is a perspective view of a wheel 2000 having a plurality offibers 2011 each of which has a chemical species immobilized thereon.The wheel 2000 has a top 2002, a bottom 2003, a perimeter sidewall 2004,and a longitudinal axis (not shown) that runs through a center wheelaperture 2006 in a direction parallel to the fibers 2011. Although thewheel 2000 may be shaped and sized to have any desired diameter andheight, it is preferred to have an aspect ratio greater than 1.0, wherethe aspect ratio is defined as a ratio of the wheel diameter to thewheel height (i.e., the vertical distance between the top 2002 and thebottom 2003 of the wheel 2000). The size of the wheel 2000 may beadjusted in order to accommodate the desired number of fibers 2011 to bedisposed thereon and the pre-determined spacing therebetween. Forexample, a wheel having a diameter of about 63 mm can accommodate on itssidewall up to 1,000 fibers (200 μm or less in diameter) whilemaintaining 200 μm of center-to-center distance between the adjacentfibers. The wheel diameter may range from 5 to 10 cm, although greateror less wheel diameters may be preferred depending on the number offibers 2011 to be disposed and desirable spacing therebetween. The wheel2000 may also include the center wheel aperture 2006 for handlingpurposes which will be discussed in greater detail below.

Still referring to FIG. 20, a plurality of the fibers 2011 are disposedon the perimeter sidewall 2004 of the wheel 2000 via mechanical and/orchemical bonding. The fibers 2011 are preferably aligned parallel toeach other and in a direction parallel to the longitudinal axis of thewheel 2000. The fibers 2011 may also be arranged to maintain a uniformspacing therebetween. The sidewall 2004 may include a plurality ofgrooves 2005, each of which extends from the top 2002 and terminates atthe bottom 2003 of the wheel 2000. The grooves 2005 are shaped and sizedto receive the fibers 2011 and to facilitate the alignment of the fibers2011. The grooves 2005 may also be shaped to retain the fibers 2011. Inaddition, it should be appreciated that the grooves may being opticallycurvatious to reflect the light into the detectors in a manner whichpromotes optimum collection efficiency. It should be appreciated thatany geometic curvature of the grooves may be used to reflect light tothe detectors.

FIG. 21 is a perspective view of a cylinder 2100 having a plurality offibers 2011 each having immobilized thereon a chemical species. Thecylinder 2100 preferably has a length much greater than its diametersuch that the fibers 2011 can be of any desired length along a surface2103 of the cylinder 2100. For example, the fibers 2011 may be 5 to 10centimeters in length on the surface 2103 of the cylinder 2100 which mayhave a diameter of about 63 mm. The cylinder 2100 may include a centercylinder aperture 2106 for ease of handling. Once disposed with thefibers 2011, the cylinder 2100 may be pre-cut and/or pre-perforated atpre-described lengths in order to pre-form a plurality of wheels 2000readily separable in a direction perpendicular to a longitudinal axis ofthe cylinder 2100. It should be appreciated that the cylinder may becomprised of separate wheels that are connected using a fastener, suchas a snap, or adhesive, such as glue or tape, so that after the fibersare placed on the cylinder, the wheel may be easily separated. The wheel2000 having a predescribed height can then be prepared by separating anend wheel unit 2000 from the rest of the cylinder 2100, for example, byapplying mechanical force, such as a knife or water jet, heat, such aslaser cutting, or by other separation methods known in the art. One ormore wheels 2000 can be separated from the cylinder 2100 with care takennot to contaminate the chemical species from one fiber onto another.Wheels 2000 and cylinders 2100 may be made of a materials similar tothat of the fiber array. The surface of the wheel 2000 and the cylinder2100 may also be provided with features such as low-fluorescence or areflective coating, for example, the cylinder may be made of plastichaving a vapor deposited gold coating.

FIG. 22 is a cross-sectional view of a wheel 2000 coupled to a wheelrotation device 2201 through a rotational coupler, such as an axle 2202positioned therebetween. By coupling one end of the axle 2202 to thewheel rotation device 2201 and by fixedly coupling the other end of theaxle 2202 to the wheel 2000 through its center wheel aperture 2006, thewheel 2000 can be rotated by the wheel rotation device 2201, such as anelectric motor, a manual rotation assembly, or other rotation devicesknown in the art. A sealing disk 2203 may be positioned between thewheel 2000 and the wheel rotation device 2201. The disk 2203 ispreferably shaped and sized according to the dimension of the containersuch that the disk 2203 may serve as a cover plate that sealinglyengages the container, as will be described later. The disk 2203 isloosely constrained by the axle 2202 which passes through a center diskaperture 2204. A bottom surface of the disk 2203 may be shaped to beconcave toward the top 2002 of the wheel 2000 in order to minimizerotational friction therebetween. A lock washer 2205 may also beprovided on top of the disk 2203 and arranged to lightly press both thewheel 2000 and the disk 2203 downwardly. It should be appreciated thatthe axle 2202 is only one example of the rotational coupler that may beused to couple the wheel 2000 to the wheel rotation device 2201. Forexample, a cylinder 2100 and a wheel 2000 may be fabricated without anycenter apertures 2006, 2106 therein. One of skill in the art wouldrecognize that such wheels 2000 without center wheel aperture 2006 canbe coupled to and rotated by the wheel rotation device 2201 using otherrotational couplers such as a vacuum chuck, magnet, and other rotatablecoupling elements known in the art.

FIG. 23 is a cross-sectional view of a container 2300 coupled to acontainer rotation device 2306. The container 2300 is capable ofreceiving and storing the mobile chemical species therein and receivingat least a portion of the perimeter sidewall 2004 of the wheel 2000. Thecontainer 2300 is preferably an open cylinder having a top opening 2301,a cavity 2302, and container sidewalls 2305. The cavity 2302 is definedby a cavity sidewall 2303 and a cavity bottom surface 2304. Because thecontainer 2300 is to receive the wheel 2000 therein, the configurationof the container 2300 is determined by the shape and size of the wheel2000. In addition, the container 2300 is also arranged to form anannular chamber gap with pre-described dimensions between the cavitysidewall 2303 and the perimeter sidewall 2004 of the wheel 2000 (thechamber gap is shown in FIG. 25, i.e., an annular ring-shaped space thatupon rotation will be filled with the mobile chemical species 2310). Thechamber gap generally has a thickness less than a few centimeters andpreferably within the range of 0.5 to 1.5 mm. The cavity bottom surface2304 may be shaped to be concave upward to minimize rotational frictionagainst the bottom, 2003 of the wheel 2000 and to preferentiallydisplace the mobile chemical species 2310 toward the cavity sidewall2303. The container 2300 is generally made of inert material andpreferably of low cost material so that it can be disposed after use.The container sidewall 2305 and/or cavity sidewall 2303 may be made offlexible material similar to that of the fiber arrays. It should beappreciated that the container may generally be made of materials thesame as or similar to the fiber arrays.

Still referring to FIG. 23, the container 2300 is mechanically coupledto the container rotation device 2306 through a platform 2307 positionedtherebetween. A top surface of the platform 2307 is shaped and sized toreceive the container 2300 such that the container rotation device 2306can rotate the platform 2307 along with the container 2300. The platform2307 may include a heating element 2311, a temperature sensor 2312 or atemperature controller 2313 for heating the fluid stored in thecontainer 2300 and controlling the temperature thereof.

FIG. 24 is a cross-sectional view of a fluid delivery system 2400according to the present invention. In general, a fluid pathway 2401 isembedded inside the wheel 2000 and terminates at one or more inlet ports2402 and outlet ports 2403. The mobile chemical species is loadedthrough the inlet port 2402, moves through the fluid pathway 2401 towardthe outlet port 2403, and is discharged into the chamber gap (shown inFIG. 25) formed between the cavity sidewall 2303 and the perimetersidewall 2004 of the wheel 2000. Gravity, capillary force, centrifugalforce, and/or electomotive force may be used as the driving force formoving the mobile chemical species through the fluid pathway 2401. Afilter (not shown) may be provided at the inlet and/or outlet ports2402, 2403, or along the fluid pathway 2401 in order to removeundesirable substances from the mobile chemical species. Filtration maybe accomplished by adsorption, absorption, filtration or other filteringmechanisms known in the art.

FIGS. 25 and 26 are a cross-sectional view and a top-plan view of afiber wheel mixing system 2500, respectively. In operation, the mobilechemical species 2310 is loaded into the cavity 2302 of the container2300 by the fluid delivery system 2400 described above (shown in FIG.31). Alternatively, the mobile chemical species 2310 may be directlyloaded into the container cavity 2302 with a syringe or pipette or byother manual or automated means. As illustrated in FIGS. 25 and 26, thefiber wheel mixing system 2500 is assembled by positioning the wheel2000 inside the container cavity 2302, by fitting the disk 2203 onto thetop opening 2301 of the container 2300, by sealingly engaging the disk2203 around the top opening 2301, and by forming a closed space forcontaining the mobile chemical species 2310. The wheel 2000 and thecontainer 2300 are rotated by the corresponding rotation devices 2201,2306. The speed and duration of the rotation may vary depending on thechemical reaction rates and may range from seconds to hours. The mobilechemical species 2310 is then displaced toward the cavity sidewall 2303by the centrifugal force, and forms an annular column of fluid 2310. Ingeneral, the thickness of the fluid column is determined by severalfactors such as the cavity diameter, cavity height, chamber gapdimension, and the amount of the mobile chemical species 2310 loadedinto the container cavity 2302. By filling the chamber gap with apre-described amount of the mobile chemical species 2310, the chemicalspecies immobilized on the fibers 2011 of the wheel 2000 can contact themobile chemical species 2310.

It is appreciated that the wheel 2000 and the container 2300 arepreferably counter-rotated at a speed enough to generate a turbulentmixing zone at the mix points. The turbulent mixing increases thecontact efficiency and minimizes the amount of the chemical speciesrequired for efficient mixing therebetween. Rotational speeds necessaryto form the turbulent mixing zone can be easily determined and confirmedby introducing an indicator or dye into the mixing zone and observingthe mixing pattern therein, or by analyzing the intensity of the lightsignals emanating from the fibers 2011 which will be discussed ingreater detail below. One of skill in the art would recognize thatrotating only one of the wheel 2000 or the container 2300 can alsogenerate a similar turbulent mixing zone.

Clearances 2501, 2502 may be provided at the contacting zones betweenthe disk 2203 and the wheel 2000, and between the wheel 2000 and thecavity bottom surface 2304. These clearances 2501, 2502 minimize therotational friction and may serve as an additional fluid channel throughwhich the mobile chemical species 2310 can be displaced during rotationfrom a cavity center toward the cavity sidewall 2303.

FIGS. 27 and 28 show two embodiments of a light evaluating system 2700for detecting light signals generated as a result of mixing two or morechemical species. The light evaluating system 2700 typically includes alight source 2701, light guiding devices 2702 a, 2702 b, and a lightdetecting device 2703. The light source 2701, such as a laser or an arclamp, produces a beam of light 2705 with the desired wavelength that isdirected to one end of the fiber 2711. Appropriate light source 2701 anddesired wavelength of the light can be selected by methods similar tothose described above in connection with the fiber array 100. Forpurposes of the present invention, the fibers 2011 are preferablyoptical fibers, details of which have already been described above. Thelight source 2701 is located under the platform 2307 such that the lightbeam 2705 is directed to the end of the fiber 2011 and internallyreflects therein. The reflected light beam 2705 creates an evanescentwave on a surface of the fiber 2011 illuminating the chemical speciesattached thereto. Because the intensity of the evanescent waveexponentially dissipates with distance from the surface of the fiber2011 (almost disappearing beyond 300 nm), the chemical species isilluminated but not the material surrounding the fiber 2011, i.e., onlythe fiber 2011 fluoresces. More specifically and as described above,only those locations along each fiber 2011 where some type ofinteraction between the chemical species has occurred will produce adetectable signal such as fluorescence. The light guiding device such asa focusing lens 2702 a and a reflecting mirror 2702 b may be used tocollect photons generated by fluorescence from the fibers 2011 and tofocus the photons into the light detecting device 2703. Examples of suchlight guiding devices include, but are not limited to, lenses, mirrors,prisms, and other optical elements known in the art. The light guidingdevice 2702 a, 2702 b as well as optional reflective coating on theperimeter sidewall 2704 of the wheel 2000 directs more photons into thelight detecting device 2703, thereby improving the signal-to-noise ratioof the detected light signals.

In operation, after measuring the light signal at a given mix point oralong a given fiber 2711, the wheel 2000 is sequentially rotated eithermanually or automatically. The rotation places a new mix point and/or anew fiber into the field of the light evaluating system 2700 and alignsthe light beam 2705 into an end of the new fiber. It is appreciated thatan optional light guiding device may be positioned between the lightsource 2701 and the platform 2307 to focus the light beam 2705 on theend of the fiber 2011. An optional motion device 2704 may be used tomove the light source 2701 and/or the light guiding devices 2702 a, 2702b along a perimeter of the wheel 2000 to properly align the light beam2705 with the end of each fiber 2011. In addition, an optional motiondetecting system with motion sensors (not shown), such as infrared lightsensors, may be used to monitor the position of the motion device 2704.

FIG. 29 shows another embodiment of a light evaluating system 2900. Thephotons collected into the light detecting device 2703 generate electriccurrent in proportion to the number of photons detected. This electricalsignal is amplified, processed, and plotted over time by an electricaldevice 2901, e.g., an oscilloscope or computer. As described above,after measuring the light signal at a given mix point or along a givenfiber 2011, the wheel 2000 is sequentially rotated and a new mix pointor a new fiber is brought into the field of the light evaluating system2900. The light beam 2705 is aligned into an end of the new fiber andthe above procedures are repeated.

FIGS. 30 and 31 illustrate another embodiment of a fiber wheel mixingsystem 3000 including a wheel assembly 3001 and a multi-cavity container3010. FIG. 30 is a cross-sectional view of the system 3000 along arotational coupler, such as a rotation axle 3002. FIG. 31 is across-sectional view of the system 3000 in a direction perpendicular tothe rotation axle 3002 of FIG. 30. The wheel assembly 3001 includesmultiple wheels 2000 vertically positioned along the rotation axle 3002through their center wheel apertures 2006, and is rotatably coupled tothe wheel rotation device 2201. The multi-cavity container 3010 consistsof a top portion 3011 and a bottom portion 3012, and each of top andbottom portions 3011, 3012 includes top and bottom dividers 3013, 3014,respectively. The top portion 3011 and top dividers 3013 are arranged tofit over the bottom portion 3012 and corresponding bottom dividers 3014such that multiple cavities 3015 form within the container 3010. Themulti-cavity container 3010 may also be rotatably coupled to thecontainer rotation device 2306.

In operation, the wheel assembly 3001 is assembled and positioned insidethe bottom portion 3012 of the multi-cavity container 3010 such thatabout a lower half of each wheel 2000 is received by a correspondingcavity 3015 of the bottom portion 3012. The top portion 3011 is thensealingly engaged over the bottom portion 3012, and each cavity 3015sealingly separates a corresponding wheel 2000 from its neighbors. Themobile chemical species 3010 is loaded into each cavity 3015 eitherdirectly with a syringe or pipette or through a fluid delivery systemsimilar to the one described in FIG. 24. At least one of the wheelassembly 3001 or the multi-cavity container 3010 is rotated by thecorresponding rotation devices 2201, 2306, thereby contacting the secondimmobilized chemical species with the mobile chemical species 3020stored in the cavities 3015. One skilled in the art would recognize thateach cavity 3015 may be loaded with different chemical species and thateach wheel 2000 may be disposed with fibers immobilized with differentchemical species. Because the processing time for multiple samples isnot much greater than that for processing a single sample, themulti-wheel-multi-chamber system of FIGS. 30 and 31 offers a benefit ofreducing labor cost per sample. It is appreciated that other featuresand advantages of the fiber wheel mixing system 2000 described in FIGS.20 through 27 equally apply to the multi-wheel-multi-chamber system 3000of FIGS. 30 and 31. For example, the wheel assembly 3001 and themulti-cavity container 3010 can be counter-rotated at a speed enough togenerate a turbulent mixing zone at the mix points.

In a further embodiment of the invention, instead of fibers, an array ofspots or dots of a chemical species may be incorporated into the wheelmixing system. These spots preferably form a cylindrical micro-array onan outer surface of a wheel. The spots may be immobilized onto adistinct substrate which is capable of transmitting light, or directlyonto the outer perimeter of the wheel itself, where the wheel is made ofa light transmitting material. The chemical species immobilized onto thesubstrate may either be directly applied onto the wheel, onto thesubstrate positioned around the circumference of the wheel or onto aflat substrate which is later conformed to the shape of the wheel. Lightentering the light transmitting material from a laser, forms anevanescent wave close to the perimeter surface of the wheel which usingthe reader described above, is used to detect binding of the chemicalspecies. The light transmitting material is preferably a glass material.

The fiber wheel mixing apparatus provides a high-quality apparatus forcontacting different chemical species. Because the fibers can be easilytested to determine the quality of immobilization of the chemicalspecies on the fiber, high quality fibers can be preferentially selectedfor use on the wheel.

In addition, the fibers of the present invention are completely driedafter being immobilized with a chemical species and before beingdisposed on the wheel. Accordingly, contamination between mix points maybe prevented, since there is little possibility of splattering onechemical species onto another, as can be the case with robot spotting.

The fiber wheel mixing apparatus is also relatively easy to use. Thesample containing a mobile chemical species is simply loaded into thecontainer with a syringe or pipette or by an appropriate fluid deliveryapparatus. The wheel is placed into the container and a rotation deviceis activated. In case post-mixing washing should be necessary, the wheelcan be removed from the container and dipped into a washing solution.Signals generated as a result of mixing can be detected and evaluated ina number of ways. The container can be discarded after use, thuseliminating the need for washing containers and reducing the potentialfor contamination.

Furthermore, by rotating both the wheel and the container in oppositedirections, the fiber wheel mixing apparatus creates a turbulent mixingzone around the mix points. The turbulent mixing dramatically increasesthe contact efficiency. Due to such a highly efficient mixing mechanism,only a minimum amount of the second immobilized chemical species isrequired for mixing and analysis, which is far less than that of moreconventional approaches.

The fiber wheel mixing apparatus also significantly improves thesignal-to-noise ratio of the signals. For example, the light detectingdevice can analyze the light signals directly emanating from the mixpoints. With little stray to cause undesirable reflections, the noisecollected by the light detecting device should be very low. In adesirable contrast, the amount of photons collected into the lightdetecting device is high because the wheel geometry, lenses, mirrors,and reflectors focus very high percentages of the light signal into thelight detecting device. The high signal-to-noise ratio also providessignificant improvement in the dynamic range and sensitivity of thefiber wheel mixing apparatus by two orders of magnitude over typicalconventional spotting techniques.

Those of skill in the art will recognize that the fiber arrays of theinvention can be used in virtually any assay where detectinginteractions between to chemical species is desired. For example, thefiber arrays can be conveniently used to screen for and identifycompounds which bind a receptor of interest, such as peptides which bindan antibody, organic compounds which bind an enzyme or receptor orcomplementary polynucleotides which bind (hybridize to) one another.However, the arrays of the invention are not limited to applications inwhich one chemical species binds another. The arrays of the inventioncan also be used to screen for and identify compounds which catalyzechemical reactions, such as antibodies capable of catalyzing certainreactions, and to screen for and identify compounds which give rise todetectable biological signals, such as compounds which agonize areceptor of interest. The only requirement is that the interactionbetween the two chemical species give rise to a detectable signal. Thus,the fiber arrays of the invention are useful in any applications thattake advantage of arrays or libraries of immobilized compounds, such asthe myriad solid-phase combinatorial library assay methodologiesdescribed in the art. For a brief review of the various assays for whichthe fiber arrays of the invention can be readily adapted, see Gallop etal., 1994, J. Med. Chem. 37:1233-1251; Gordon et al., 1994, J. Med.Chem. 37:1385-1401; Jung, 1992, Agnew Chem. Pat. Ed. 31:367-386;Thompson & Ellman, 1996, Chem Rev. 96: 555-600, and the references citedin all of the above.

The fiber arrays of the invention are particularly useful forapplications involving hybridization of nucleic acids, especially thoseapplications involving high density arrays of immobilizedpolynucleotides, including, for example, de novo sequencing byhybridization (SBH) and detection of polymorphisms. In theseapplications, conventional immobilized polynucleotide arrays typicallyused in the art can be conveniently and advantageously replaced with thefiber arrays of the invention. For a review of the various array-basedhybridization assays in which the fiber arrays of the invention finduse, see U.S. Pat. Nos. 5,202,231; 5,525,464; WO 98/31836, and thereferences cited in all

Based on the above, those of skill in the art will recognize that thechemical species immobilized on the fiber can be virtually any types ofcompounds, ranging from organic compounds such as potential drugcandidates, polymers and small molecule inhibitors, agonists and/orantagonists, to biological compounds such as polypeptides,polynucleotides, polycarbohydrates, lectins, proteins, enzymes,antibodies, receptors, nucleic acids, etc. The only requirement is thatthe chemical species be capable of being immobilized on the fiber.

In a preferred embodiment, the chemical species immobilized on the fiberis a polynucleotide. Typically, the polynucleotide will be of astrandedness and length suitable for format II and format III SBH andrelated applications. Thus, the polynucleotide will generally besingle-stranded and be composed of between about 4 to 30, typicallyabout 4 to 20, and usually about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or20 nucleotides. However, it will be recognized that the fiber arrays ofthe invention are equally well suited for use with format I SBH, andrelated applications, where an immobilized target nucleic acid isinterrogated with solution-phase oligonucleotide probes. Thus, thepolynucleotide can be any number of nucleotides in length and be eithersingle- or double-stranded, depending on the particular application.

The polynucleotide may be composed entirely of deoxyribonucleotides,entirely of ribonucleotides, or may be composed of mixtures of deoxy-and ribonucleotides. However, due to their stability to RNases and hightemperatures, as well as their ease of synthesis, polynucleotidescomposed entirely of deoxyribonucleotides are preferred.

The polynucleotide may be composed of all natural or all syntheticnucleotide bases, or a combination of both. While in most instances thepolynucleotide will be composed entirely of the natural bases (A, C, G,T or U), in certain circumstances the use of synthetic bases may bepreferred. Common synthetic bases of which the polynucleotide may becomposed include 3-methlyuracil, 5,6-dihydrouracil, 4-thiouracil,5-bromouracil, 5-thorouracil, 5-iodouracil, 6-dimethyl amino purine,6-methyl amino purine, 2-amino purine, 2,6-diamino purine,6-amino-8-bromo purine, inosine, 5-methyl cytosine, and 7-deazaquanosine. Additional non-limiting examples of synthetic bases of whichthe polynucleotide can be composed can be found in Fasman, CRC PracticalHandbook of Biochemistry and Molecular Biology, 1985, pp. 385-392.

Moreover, while the backbone of the polynucleotide will typically becomposed entirely of “native” phosphodiester linkages, it may containone or more modified linkages, such as one or more phosphorothioate,phosphoramidite or other modified linkages. As a specific example, thepolynucleotide may be a peptide nucleic acid (PNA), which contains amideinterlinkages. Additional examples of modified bases and backbones thatcan be used in conjunction with the invention, as well as methods fortheir synthesis can be found, for example, in Uhlman & Peyman, 1990,Chemical Review 90(4):544-584; Goodchild, 1990, Bioconjugate Chem.1(3):165-186; Egholm et al., 1992, J. Am. Chem. Soc. 114:1895-1897;Gryaznov et al., J. Am. Chem. Soc. 116:3143-3144, as well as thereferences cited in all of the above.

While the polynucleotide will often be a contiguous stretch ofnucleotides, it need not be. Stretches of nucleotides can be interruptedby one or more linker molecules that do not participate insequence-specific base pairing interactions with a target nucleic acid.The linker molecules may be flexible, semi-rigid or rigid, depending onthe desired application. A variety of linker molecules useful forspacing one molecule from another or from a solid surface have beendescribed in the art (and have been described more thoroughly supra);all of these linker molecules can be used to space regions of thepolynucleotide from one another. In a preferred embodiment of thisaspect of the invention, the linker moiety is from one to ten,preferably two to six, alkylene glycol moieties, preferably ethyleneglycol moieties.

The polynucleotide can be isolated from biological samples, generated byPCR reactions or other template-specific reactions, or madesynthetically. Methods for isolating polynucleotides from biologicalsamples and/or PCR reactions are well-known in the art, as are methodsfor synthesizing and purifying synthetic polynucleotides.Polynucleotides isolated from biological samples and/or PCR reactionsmay, depending on the desired mode of immobilization, requiremodification at the 3′- or 5′-terminus, or at one or more bases, as willbe discussed more thoroughly below. Moreover, since the polynucleotidemust typically be capable of hybridizing to another target nucleic acid,if not already single stranded, it should preferably be rendered singlestranded, either before or after immobilization on the fiber.

Depending on the identity of the chemical species and the fibermaterial, the chemical species can be immobilized by virtually any meansknown to be effective for immobilizing the particular type of chemicalspecies on the particular type of fiber material. For example, thechemical species can be immobilized via absorption, adsorption, ionicattraction or covalent attachment. The immobilization may also bemediated by way of pairs of specific binding molecules, such as biotinand avidin or streptavidin. Methods for immobilizing a variety ofchemical species to a variety of materials are known in the art. Any ofthese art-known methods can be used in conjunction with the invention.

For adsorption or absorption, fiber 11 can be conveniently prepared bycontacting the fiber with the chemical species to be immobilized for atime period sufficient for the chemical species to adsorb or absorb ontothe fiber. Following optional wash steps, the fiber is then dried. Whenthe chemical species is a polynucleotide, the various methods describedin the dot-blot or other nucleic acid blotting arts for immobilizingnucleic acids onto nitrocellulose or nylon filters can be convenientlyadapted for use in the present invention.

For immobilization by ionic attraction, if not inherently charged, thefiber is first activated or derivatized with charged groups prior tocontacting it with the chemical species to be immobilized, which iseither inherently oppositely charged or has been modified to beoppositely charged.

For immobilization mediated by way of specific binding pairs, the fiberis first derivatized and/or coated with one member of the specificbinding pair, such as avidin or streptavidin, and the derivatized fiberis then contacted with a chemical species which is linked to the othermember of the specific binding pair, such as biotin. Methods forderivatizing or coating a variety of materials with binding moleculessuch as avidin or streptavidin, as well as methods for linking myriadtypes of chemical species to binding molecules such as biotin are wellknown in the art. For polynucleotide chemical species, biotin can beconveniently incorporated into the polynucleotide at either a terminaland/or internal base, or at one or both of its 5′- and 3′-termini usingcommercially available chemical synthesis or biological synthesisreagents.

In a preferred embodiment of the invention, the chemical species iscovalently attached to the fiber, optionally be way of one or morelinking moieties. Unless the fiber inherently contains reactivefunctional groups capable of forming a covalent linkage with thechemical species, it must first be activated or derivatized with suchreactive groups. Typical reactive groups useful for effecting covalentattachment of chemical species to the fiber include hydroxyl, sulfonyl,amino, cyanate, isocyanate, thiocyanate, isothiocyanate, epoxy andcarboxyl groups, although other reactive groups as will be apparent tothose of skill in the art may also be used.

A variety of techniques for activating myriad types of fiber materialswith reactive groups suitable for covalently attaching chemical speciesthereto, particularly biological molecules such as polypeptides,proteins, polynucleotides and nucleic acids, are known in the art andinclude, for example, chemical activation, corona discharge activation;flame treatment activation; gas plasma activation and plasma enhancedchemical vapor deposition. Any of these techniques can be used toactivate the fiber with reactive groups. For a review of the manytechniques that can be used to activate or derivatize the fiber, seeWiley Encyclopedia of Packaging Technology, 2d Ed., Brody & Marsh, Ed.,“Surface Treatment,” pp. 867-874, John Wiley & Sons, 1997, and thereferences cited therein. Chemical methods suitable for generating aminogroups on preferred glass optical fibers are described in Atkinson &Smith, “Solid Phase Synthesis of Oligodeoxyribonucleotides by thePhosphite Triester Method,” In: Oligonucleotide Synthesis: A PracticalApproach, M J Gait, Ed., 1985, IRL Press, Oxford, particularly at pp.45-49 (and the references cited therein); chemical methods suitable forgenerating hydroxyl groups on preferred optical glass fibers aredescribed in Pease et al., 1994, Proc. Natl. Acad. Sci. USA 91:5022-5026(and the references cited therein); chemical methods suitable forgenerating functional groups on fiber materials such as polystyrene,polyamides and grafted polystyrenes are described in Lloyd-Williams etal., 1997, Chemical Approaches to the Synthesis of Peptides andProteins, Chapter 2, CRC Press, Boca Raton, Fla. (and the referencescited therein). Additional methods are well-known, and will be apparentto those of skill in the art.

For fibers coated with a conductor, such as gold, the chemical speciescan be attached to the conductor using known chemistries. For example, apolynucleotide can be covalently attached to a gold-coated fiber usingthe methods described in Herne & Taylor, 1997, J. Am. Chem. Soc.119:8916-8920. This chemistry can be readily adapted for covalentlyimmobilizing other types of chemical species onto a gold-coated fiber.

Depending on the nature of the chemical species, it can be covalentlyimmobilized on the activated fiber following synthesis and/or isolation,or, where suitable chemistries are known, it may be synthesized in situdirectly on the activated fiber. For example, a purified polypeptide maybe covalently immobilized on an amino-activated fiber, conveniently byway of its carboxy terminus or a carboxyl-containing side chain residue.Alternatively, the polypeptide can be synthesized in situ directly on anamino-activated fiber using conventional solid-phase peptide chemistriesand reagents (see Chemical Approaches to the Synthesis of Peptides andProteins, Lloyd-Williams et al., Eds., CRC Press, Boca Raton, Fla., 1997and the references cited therein). Similarly, a purified polynucleotidebearing an appropriate reactive group at one or more of its bases ortermini can be covalently immobilized on an isothiocyanate- orcarboxy-activated fiber, or alternatively, the polynucleotide can besynthesized in situ directly on a hydroxyl-activated fiber usingconventional oligonucleotide synthesis chemistries and reagents (seeOligonucleotide Synthesis: A Practical Approach, 1985, supra, and thereferences cited therein). Other types of compounds which can beconveniently synthesized by solid phase methods can also be synthesizedin situ directly on a fiber. Non-limiting examples of compounds whichcan be synthesized in situ include Bassenisi and Ugi condensationproducts (WO 95/02566), peptoids (Simon et al., 1992, Proc. Natl. Acad.Sci. USA 89:9367-9371), non-peptide non-oligomeric compounds (Dewitt etal., 1993, Proc. Natl. Acad. Sci. USA 90:6909-6913) and 1,4benzodiazepines and derivatives (Bunin et al., 1994, Proc. Natl. Acad.Sci. USA 91:4708-4712); Bunin & Ellman, 1992, J. Am. Chem. Soc.114:10997-10998).

Those of skill in the art will recognize that when using in situchemical synthesis, the covalent bond formed between the immobilizedchemical species and the fiber must be substantially stable to thesynthesis and deprotection conditions so as to avoid loss of thechemical species during synthesis and/or deprotection. Forpolynucleotides, one such stable bond is the phosphodiester bond, whichconnects the various nucleotides in a polynucleotide, and which can beconveniently formed using well-known chemistries (see, e.g.,Oligonucleotide Synthesis: A Practical Approach, 1985, supra). Otherstable bonds suitable for use with hydroxyl-activated fibers includephosphorothiate, phosphoramidite, or other modified nucleic acidinterlinkages. For fibers activated with amino groups, the bond could bea phosphoramidate, amide or peptide bond. For fibers activated withepoxy functional groups, a stable C—N bond could be formed. Suitablereagents and conditions for forming such stable bonds are well known inthe art.

In one particularly convenient embodiment, a polynucleotide isimmobilized on a fiber by in situ synthesis on a hydroxyl-activatedfiber using commercially available phosphoramidite synthesis reagentsand standard oligonucleotide synthesis chemistries. In this mode, thepolynucleotide is covalently attached to the activated fiber by way of aphosphodiester linkage. The density of polynucleotide covalentlyimmobilized on the filter can be conveniently controlled by adding anamount of the first synthon (e.g., N-protected5′-O-dimethoxytrityl-2′-deoxyribonucleotide-3′-O-phosphoramidite)sufficient to provide the desired number of synthesis groups on thefiber, and capping any unreacted hydroxyl groups on the fiber with acapping reagent (e.g., 1,4-diaminopyridine; DMAP). After the excesshydroxyls have been capped, the trityl group protecting the 5′-hydroxylcan be removed and synthesis of the polynucleotide carried out usingstandard techniques. Following synthesis, the polynucleotide isdeprotected using conventional methods.

In an alternative embodiment, a polynucleotide is covalently attached tothe activated fiber through a post-synthesis or post-isolationconjugation reaction. In this embodiment, a pre-synthesized or isolatedpolynucleotide which is modified at its 3′-terminus, 5-terminus and/orat one of its bases with a reactive functional group (e.g. epoxy,sulfonyl, amino or carboxyl) is conjugated to an activated fiber via acondensation reaction, thereby forming a covalent linkage. Again,substantially stabile (i.e., non-labile) covalent linkages such asamide, phosphodiester and phosphoramidate linkages are preferred.Synthesis supports and synthesis reagents useful for modifying the 3′-and/or 5′-terminus of synthetic polynucleotides, or for incorporating abase modified with a reactive group into a synthetic polynucleotide, arewell-known in the art and are even commercially available.

For example, methods for synthesizing 5′-modified oligonucleotides aredescribed in Agarwal et al., 1986, Nucl. Acids Res. 14:6227-6245 andConnelly, 1987, Nucl. Acids Res. 15:3131-3139. Commercially availableproducts for synthesizing 5′-amino modified oligonucleotides include theN-TFA-C6-AminoModifer™, N-MMT-C6-AminoModifer™ andN-MMT-C12AminoModifier™ reagents available from Clontech Laboratories,Inc., Palo Alto, Calif.

Methods for synthesizing 3′-modified oligonucleotides are described inNelson et al., 1989, Nucl. Acids Res. 17:7179-7186 and Nelson et al.,1989, Nucl. Acids Res. 17:7187-7194. Commercial products forsynthesizing 3′-modified oligonucleotides include the 3′-Amino-ON™controlled pore glass and Amino Modifier II™ reagents available fromClontech Laboratories, Inc., Palo Alto, Calif.

Other methods for modifying the 3′and/or 5′termini of oligonucleotides,as well as for synthesizing oligonucleotides containing appropriatelymodified bases are provided in Goodchild, 1990, Bioconjugate Chem.1:165-186, and the references cited therein. Chemistries for attachingsuch modified oligonucleotides to materials activated with appropriatereactive groups are well-known in the art (see, e.g., Ghosh & Musso,1987, Nucl. Acids Res. 15:5353-5372; Lund et al., 1988, Nucl. Acids Res.16:10861-10880; Rasmussen et al., 1991, Anal. Chem. 198:138-142; Kato &Ikada, 1996, Biotechnology and Bioengineering 51:581-590; Timofeev etal., 1996, Nucl. Acids Res. 24:3142-3148; O'Donnell et al., 1997, Anal.Chem. 69:2438-2443).

Methods and reagents for modifying the ends of polynucleotides isolatedfrom biological samples and/or for incorporating bases modified withreactive groups into nascent polynucleotides are also well-known andcommercially available. For example, an isolated polynucleotide can bephosphorylated at its 5′-terminus with phosphorokinase and thisphosphorylated polynucleotide covalently attached onto anamino-activated fiber through a phosphoramidate or phosphodiesterlinkage. Other methods will be apparent to those of skill in the art.

In one convenient embodiment of the invention, a polynucleotide modifiedat its 3′- or 5′-terminus with a primary amino group is conjugated to acarboxy-activated fiber. Chemistries suitable for forming carboxamidelinkages between carboxyl and amino functional groups are well-known inthe art of peptide chemistry (see, e.g., Atherton & Sheppard, SolidPhase Peptide Synthesis, 1989, IRL Press, Oxford, England andLloyd-Williams et al., Chemical Approaches to the Synthesis of Peptidesand Proteins, 1997, CRC Press, Boca Raton, Fla. and the references citedtherein). Any of these methods can be used to conjugate anamino-modified polynucleotide to a carboxy-activated fiber.

In one embodiment, the carboxamide linkage is generated usingN,N,N′,N′-tetramethyl (succinimido) uronium tetrafluoroborate (“TSTU”)as a coupling reagent. Reaction conditions for the formation ofcarboxyamides with TSTU that can be used in conjunction with nucleicacids are described in Knorr et al., 1989, Tet. Lett. 30(15):1927-1930;Bannworth & Knorr, 1991, Tet. Lett. 32(9):1157-1160; and Wilchek et al.,1994, Bioconjugate Chem. 5(5):491-492.

Whether synthesized directly on the activated fiber or immobilized onthe activated fiber post-synthesis or post-isolation, the chemicalspecies can optionally be spaced away from the porous substrate by wayof one or more linkers. As will be appreciated by those having skill inthe art, such linkers will be at least bifunctional, i.e., they willhave one functional group or moiety capable of forming a linkage withthe activated fiber and another functional group or moiety capable offorming a linkage with another linker molecule or the chemical species.The linkers may be long or short, flexible or rigid, charged oruncharged, hydrophobic or hydrophilic, depending on the particularapplication.

In certain circumstances, such linkers can be used to “convert” onefunctional group into another. For example, an amino-activated fiber canbe converted into a hydroxyl-activated fiber by reaction with, forexample, 3-hydroxypropionic acid. In this way, fiber materials whichcannot be readily activated with a specified reactive functional groupcan be conveniently converted into a an appropriately activated fiber.Chemistries and reagents suitable for “converting” such reactive groupsare well-known, and will be apparent to those having skill in the art.

Linkers can also be used, where necessary, to increase or “amplify” thenumber of reactive groups on the activated fiber. For this embodiment,the linker will have three or more functional groups. Followingattachment to the activated fiber by way of one of the functionalgroups, the remaining two or more groups are available for attachment ofthe chemical species. Amplifying the number of functional groups on theactivated fiber in this manner is particularly convenient when theactivated fiber contains relatively few reactive groups.

Reagents for amplifying the number of reactive groups are well-known andwill be apparent to those of skill in the art. A particularly convenientclass of amplifying reagents are the multifunctional epoxides sold underthe trade name DENACOL™ (Nagassi Kasei Kogyo K.K.). These epoxidescontain as many as four, five, or even more epoxy groups, and can beused to amplify fibers activated with reactive groups that react withepoxides, including, for example, hydroxyl, amino and sulfonyl activatedfibers. The resulting epoxy-activated fibers can be convenientlyconverted to a hydroxyl-activated fiber, a carboxy-activated fiber, orother activated fiber by well-known methods.

Linkers suitable for spacing biological or other molecules, includingpolypeptides and polynucleotides, from solid surfaces are well-known inthe art, and include, by way of example and not limitation, polypeptidessuch as polyproline or polyalanine, saturated or unsaturatedbifunctional hydrocarbons such as 1-amino-hexanoic acid and polymerssuch as polyethylene glycol, etc. For polynucleotide chemical species, aparticularly preferred linker is polyethylene glycol (MW 100 to 1000).1,4-Dimethoxytrityl-polyethylene glycol phosphoramidites useful forforming phosphodiester linkages with hydroxyl groups ofhydroxyl-activated fibers, as well as methods for their use in nucleicacid synthesis on solid substrates, are described, for example in Zhanget al., 1991, Nucl. Acids Res. 19:3929-3933 and Durand et al., 1990,Nucl. Acids Res. 18:6353-6359. Other methods of attaching polyethyleneglycol linkers to activated fibers will be apparent to those of skill inthe art.

Regardless of the mode of immobilization, fibers 11 can be prepared in abatch-wise fashion where lengths of fiber are immersed in the solutionsnecessary to effect immobilization of the chemical species.Alternatively, fibers 11 can be prepared in a flow-through method inwhich the fiber is continuously flowed through reservoirs containing thesolutions necessary to effect immobilization.

FIG. 32 is one embodiment for preparation of the fiber for use in thefiber array according to the present invention in a batch-wise fashion.The fibers 3202 are attached to a fiber holder 3204 comprising fibergrippers 3206 which hold the fiber 3202. The fiber holder 3204 permitsthe fiber to be easily supported and transported and can be attached toany mechanical device (not shown) to automatically transport the fibers3202. A dipping vessel 3208 is a vessel that can contains a fluid to becontacted with the fibers 3202. In operation, the fibers 3202 areattached to the fiber grippers 3206, and the fiber holder 3204 lowersthe fibers 3202 into a solution contained in the dipping vessel 3208.The fiber holder 3204 then removes the fibers 3202 from the dippingvessel 3208. It should be appreciated that the fibers may besequentially placed into different dipping vessels each containingdifferent solutions depending upon the chemical species to beimmobilized on the fibers and the method used for immobilization. Afterthe chemical species has been immobilized on the fibers, the fibers maybe loaded onto a support plate or stored for future use. If the fibersare stored, refrigeration may be necessary depending upon the chemicalspecies on the fibers.

It is projected that with the present invention, once the fibers havebeen prepared as described, 100 fibers, each 10 cm in length, could belaid per second on a 10 cm support plate thereby producing 1,000,000contact points. It should be appreciated that laying the fibers on thesupport plate only requires accurate placement in a direction parallelto the channels to insure the fiber rests in the grooves on the channelwalls. Since the fiber can be placed anywhere in the direction parallelto the fiber, placing the fiber on the support plate is relativelysimple.

FIG. 33 is a process flow diagram of another embodiment for preparationof the fiber in a flow-through method for use in the fiber arrayaccording to the present invention. A motor 3301 is used to pull a fiber3304 from a fiber spool 3302 containing a length of material desired tobe used for the fibers 3304. If it is desired to coat the fiber 3304with a conductive coating, the fiber 3304 is first pulled through aconductive coating vat 3306 which contains a pool of conductive materialto be coated on the fiber 3304. More specifically, the conductivecoating vat 3306 utilizes meniscus coating to apply the conductivecoating to the fiber 3304, wherein the fiber 3304 is pulled through anarrow opening 3307 which only permits a thin layer of metal coating tobe applied to the fiber 3304. It should be appreciated that a conductivecoating is not required for use of the fiber array of the presentinvention. However, to utilize electro-osmosis, a metal or electricallyconductive oxide coating is preferred.

The fiber 3304 is then passed through a series of coating vats 3308,3310 depending upon the chemical species to be immobilized on the fibersand the method used for immobilization. Each coating vat may contain adifferent solution required to prepare the fiber and immobilize a givenchemical species on the fiber.

Lastly, the fiber 3304 is fed past the motor 3301 and is cut intodesired lengths by cutting apparatus 3312. It should be appreciated thatany length of fiber may be generated depending upon the size of thefiber array matrix. The cutting apparatus 3312 may be a laser or othermeans known in the art for cutting fibers or optical fibers. It shouldbe appreciated that it is important to obtain a very clean and straightcut if the fiber 3304 is an optical fiber so that in use the beam oflight directed at the end of the fiber is able to enter the fiber at thecorrect angle. Once cut, the fibers 1404 may be loaded onto a supportplate or stored for later use. If the fibers are stored, refrigerationmay be necessary depending upon the materials deposited on the fibers.

Following preparation by either of the methods described above, a lengthof fiber can be conveniently analyzed to verify the quality of theimmobilization process. For example, the chemical species immobilized ona portion of the fiber can be removed using conventional means andanalyzed using any of a variety of analytical techniques, including, forexample, gel electrophoresis (for polypeptides and polynucleotides),nuclear magnetic resonance, column chromatography, mass spectroscopy,gas chromatography, etc. Of course, the actual analytical means used toanalyze the fiber will depend on the nature of the chemical speciesattached thereto, and will be apparent to those of skill in the art.

While not preferred, fibers 110 may also be prepared, i.e., the chemicalspecies may be immobilized to the fibers, while the fibers are disposedwithin the fiber array. In this embodiment, once the fibers are disposedin the support plate, the various fluids necessary to activate and/orimmobilize the chemical species to the fiber are flowed into channels108 to contact the fiber. This method is particularly convenient when itis desirable to immobilize different chemical species at differentspatial addresses along the length of the fiber.

The present invention is further directed to an apparatus and method forsynthesizing a chemical compound on a fiber. The synthesized fibers arethen used to fabricate fiber arrays discussed supra. This apparatus is afiber array multiplicative synthesizer that implements a direct processof moving a fiber through a plurality of coating modules that synthesizeone base onto the fiber. The coating modules can be stacked into columnswith a fiber passing out of one module into the next module. Each modulesequentially adds one base to the oligo. In one configuration, manycolumns of coating modules can be grouped into hubs, and those hubs canbe rotated relative to each other such that the number of differentoligos generated is much greater than the number of coating modulesdeployed, thus the name multiplicative synthesis. The fibers extractedfrom the multiplicative synthesizer system are directly loaded into afiber array. After sealing, the fiber array is immediately ready as ananalysis tool. In a second configuration, the modules are programmableto provide complex oligo configurations on-demand.

FIG. 34 is a diagrammatic drawing of a multiplicative fiber arraysynthesizer 3420 according to the present invention. The fiber arraysynthesizer 3420 comprises at least one, but preferably a plurality of,depositors 3422 where each of the depositors 3422 is capable ofdepositing a chemical species on a fiber 3426. The depositors 3422, asexplained in further detail below, may comprise a plurality of baths,spray chambers, wicking mechanisms, or the like. The multiplicativefiber array synthesizer 3420 further comprises a transporter 3424. Thetransporter 3424 may bring the fiber 3426 and the depositors 3422 intoproximity with one another, as indicated by control lines 3430, in orderto deposit at least one chemical species precursor on the fiber 3426 toform the chemical species. The transporter 3424 may move the depositors3422 into proximity with the fiber 3426, the fiber 3426 into proximitywith the depositors 3422, or both the depositors 3422 and the fiber 3426relative to one another. Alternatively, the transporter may comprise afluid delivery system for delivering the chemical species precursors toeach of said depositors 3422 the control of which is again indicated bythe control lines 3430. Specific examples of the transporter 3424 willbe discussed in further detail below. A selector 3428 controls the orderin which each of the at least one chemical species precursor isdeposited on the fiber 3426 from each of the depositors 3422. This maybe done by controlling the transporter 3424 to move the depositors 3422into proximity with the fiber 3426 in a predetermined order or bycontrolling the transporter 3424 to move the fiber 3426 into proximitywith the depositors 3422 in a predetermined order. The selector 3428 mayalso control the order in which each of the at least one chemicalspecies precursor is supplied to each of the depositors 3422 by thefluid delivery system.

FIG. 35A is a side view of one embodiment of depositors 3422 shown inFIG. 34. In this embodiment, each of the depositors 3422 comprise of atleast one bath 3532 containing a chemical species precursor 3536. Thechemical species precursor 3536 may for example comprise of a solutioncontaining phosphoramodites or other solutions such as washing solvents.In a preferred embodiment, the transporter 3424 of FIG. 34 comprises adipping mechanism for positioning the fiber 3526 in the bath 3532. Thedipping mechanism may comprise a conveyor system such as a series ofrollers 3538 and 340 which frictionally engage with the fiber 3526 topush the fiber 3526 through the bath 3532 and hence into contact withthe chemical species 3536. The dipping mechanism may alternativelycomprise a mechanism for dipping substantially straight lengths, orcoils of the fiber 3526 directly into the bath 3532 and the chemicalspecies 3536. The fiber 3526 may be wound multiple times around animmersed roller 3540 to vary the resonance time of the fiber 3526, asthe fiber 3526 is moved through the bath 3532 at a constant speed. Thismeans that the more times the fiber 3526 is wound around the roller3540, the longer the fiber 3526 is exposed to the chemical species 3536.The roller 3540 may comprise of a cage like device which allows allpoints along the fiber 3526 at some time or another, to be exposed tothe chemical species 3536.

FIG. 35B is a perspective view of another embodiment of the invention.In this embodiment, the transporter 3424 of FIG. 34 comprises a bathtransporter 3542 for moving the bath 3532, such that the chemicalspecies precursor 3536 is brought into contact with the fiber 3526.

FIG. 35C is a side view of yet another embodiment of the invention. Inthis embodiment, the transporter 3424 of FIG. 34 comprises a fluiddelivery system 3544 which delivers different chemical speciesprecursors or solutions into 3530 and out of 3548 the bath 3532.

FIG. 36A is a side view of an embodiment of depositors 3422 shown inFIG. 34. In this embodiment, each of the depositors 3422 comprise of atleast one spray chamber 3654 and a spray mechanism 3644 for spraying thechemical species precursor 3646 onto the fiber 3526. Again the chemicalspecies precursor 3646 may for example comprise of a solution containingphosphoramodites or other solutions such as washing solvents. In oneembodiment, the transporter 3424 of FIG. 34 comprises a fibertransportation mechanism such as a conveyor system 3656 whichfrictionally engages with the fiber 3526 to push the fiber 3526 throughthe spray chamber 3654.

FIG. 36B is a side view of another embodiment of depositors 3422 shownin FIG. 34. The transporter 3424 of FIG. 34 may alternatively compriseof a spray chamber transporter 3650 for bringing the spray chamber 3654into proximity with the fiber 3526.

FIG. 36C is a side view of yet another embodiment of depositors 3422shown in FIG. 34. In this embodiment, the transporter 3424 of FIG. 34comprises a fluid delivery system 3658 which delivers 3660 differentchemical species precursors or solutions to the spray mechanism 3644.

FIG. 37A is a side view of an embodiment of depositors 3422 shown inFIG. 34. In this embodiment, each of the depositors 3422 comprise of atleast one wicking mechanism 3762 for wicking a chemical speciesprecursor 3764 onto the fiber 3526. Yet again the chemical speciesprecursors may for example comprise of a solution containingphosphoramodites or other solutions such as washing solvents. Thetransporter 3424 of FIG. 34 comprises a fiber transportation mechanismsuch as a conveyor system 3766 which frictionally engages with the fiber3526.

FIG. 37B is a side view of another embodiment of depositors 3422 shownin FIG. 34. The transporter 3424 of FIG. 34 comprises a wickingmechanism transporter 3760 for bringing the wicking mechanism 3762 intoproximity with the fiber 3526.

FIG. 37C is a side view of another embodiment of depositors 3422 shownin FIG. 34. The transporter 3524 of FIG. 34 comprises a fluid deliverysystem 3770 which delivers different chemical species or solutions tothe wicking mechanism 3762.

In each of the above embodiments shown in FIGS. 35A to 37C, a mechanismto vary the resonance time of the fiber 3526 may be provided. Theselector 3428 of FIG. 34 may controls the transporter, in all of it'salternative embodiments, to vary the order in which each of theplurality of chemical species precursors are deposited on the fiber3526.

FIG. 38 is a perspective view of a preferred embodiment of theinvention, namely a fiber array multiplicative synthesizer 3802.Multiple spools 3804 containing reeled-up fiber 3806 are mounted on arotary platform 3808. The fibers 3806 typically comprise a flexiblethread like material, such as for example plastic or glass, and arewrapped around spools 3804 such that many meters can be stored butreadily retrieved. The spools 3804 are equally spaced in a circularpattern about the platform 3808 with the fibers 3806 passing through theplatform 3808. The platform 3808 is fixed to motor 3810, and the motor3810 is fixed to a support shaft 3812 that passes through the centers ofthe platform 3808 and both hubs 3814, 3818. Motor 3816 is also fixed tothe support shaft 3812. The platform 3808 is rotatable about the supportshaft 3812. The platform 3808 maybe rotated by a first rotation means3810, such as a motor or the like. An upper hub 3814 is also rotatableabout the support shaft 3812 and may be rotated by a second rotationmeans 3816 , such as a motor or the like. A lower hub 3818 is alsorotatable about the support shaft 3812 and may be rotated by a thirdrotation means (not shown), such as a motor or the like. Hubs 3814 and3818 both contain multiple coating modules 3820, preferably arranged ina cylindrical manner about support shaft 3812. Each coating module 3820further comprises a series of depositors (best seen in FIG. 40)extending radially from the support shaft 3812. The fibers 3806continuously pass through a set of coating modules 3820 with each module3820 synthesizing a predetermined chemistry sequence or compound ontothe fiber. The fibers 3806 pass through both hubs 3814 and 3818. Fibercutting devices 3822 (best seen in FIG. 39) are provided between theplatform 3808 and hub 3814 and between hubs 3814 and 3818. The fibercutting devices 3822 sever the fibers 3806 when a new synthesis sequenceor chemical compound is desired. After the fibers 3806 pass through bothhubs 3814 and 3818, they enter a deprotection/quality-control module3824 and thereafter are supplied to the end-product, for example anotherspool or a fiber array 3826. A motor 3828 moves the end-product toposition multiple fibers thereon. It should be appreciated that hubs3814 and 3818 are preferably cylindrical but may be of any suitableshape.

Corresponding to the circular arrangement of the fiber spools 3804, thecoating modules 3820 are arranged to receive fiber 3806, continuouslysynthesizing one compound onto it, and output the fiber 3806 such thatit can be introduced into an adjacent coating module 3820. For eachfiber 3806, the modules 3820 are stacked on top of one another togenerate the desired synthesis or compound. When a new synthesissequence for the fibers 3806 is desired, the cutting modules 3822 (FIG.39) sever each fiber 3806, and the lower hub 3818 is rotated relative tothe upper hub 3814. This rotation of the lower hub 3818 causes thefibers 3806 from the upper hub 3814 to enter another module in the lowerhub 3818 as the fibers 3806 of cut-length continues to pass through thelower hub 3818. In other words, the motion of fiber 3806 through thesystem is not interrupted to change to a new synthesis sequence. Thefiber may initially be manually fed through the modules, and once thefiber is cut, the fiber from the upper hub may naturally feed into thelower hub after it has rotated. Alternatively, the fiber may be fusedwith the end of an adjacent fiber located in the lower hub after it hasbeen rotated. The fusing of fiber ends may be accomplished bymechanical, chemical or thermal means.

FIG. 39 is an enlarged perspective view of the fiber cutting device 3822illustrated in FIG. 38. The fiber cutting device 3822 consists of a top3902 and bottom 3904 circular saw blades in the location between theplatform 3808 and the upper hub 3814. The top blade 3902 may be fixed tothe motor 3810 that rotates the platform 3808 about the support shaft3812. The bottom blade 3904 may be fixed to the stationary hub 3814.When the platform 3808 rotates to a new position, the fiber cuttingdevice 3822 cuts all the fibers 3806 simultaneously between the platform3808 and the upper hub 3814. A similar fiber cutting device 3822 mayalso be located between hubs 3814 and 3818. The top blade 3902 of thefiber cutting device 3822 may be fixed to the upper hub 3814. The bottomblade 3904 rotates with the lower hub 3818, cutting the fibers 3806 asit rotates.

FIG. 40 is a side view of the coating module illustrated in FIG. 38. Thecoating module 3820 preferably consists of multiple containers 4002containing liquids. 4004-4016 through which a fiber 3806 may becontinuously passed. The fiber 3806 is guided through the liquids4004-4016 by small rollers 4018 and large rollers 4020. The liquids4004-4016 are of the correct chemical composition and concentration toadd a DNA base to the fiber 3806. A preferred arrangement of liquids4004-4016, listed in order of fiber contact, are: detritylation 4004,activator 4006, phosphoramidite (base) 4008, capping agent A & B 4010,washing solution 4012, oxidizer 4014, and a second washing solution4016. The fiber 3806 preferably exits the coating module 3820 at thesame rate that it enters, and at a composition that allows a subsequent(or the same) module 3820 to chemically add or synthesize another baseonto the DNA chain.

A plurality of modules 3820 can be stacked to add as many DNA bases ontoa fiber 3806 as desired. For example, FIG. 41 shows three modules4100-4104 stacked so as to synthesize three bases onto the fiber 3806.The fiber 3806 is introduced from a spool 3804 that may contain manymeters of fiber 3806.

After the bases are synthesized onto the fiber 3806, the fiber 3806passes through a deprotection module 3824 where protection chemicals areremoved. The removal process releases a small percentage of oligos thatare tested by quality control sensors 4108. After deprotection, thefiber 3806 is positioned in channels on a plurality of fiber arraysubstrates 3826. A motor 3828 moves the fiber arrays 3826 such that thefibers fill all of the channels. Cutting means 4110 are provided beforeand between the fiber arrays 3826 to sever the fiber into shortsegments.

FIG. 42 is an enlarged side view of the deprotection module illustratedin FIG. 38. The deprotection module 3824 removes deprotection groups4208 that were added to an oligo 4210 during synthesis. This removal isimplemented by exposing the oligos 4210 to a deprotection composition4212 such as methyl aminine, to dissolve the deprotection groups 4208.In addition, to removing deprotection groups 4208, some of the oligos4218 are extracted from the fiber 3806 for quality control purposes.This removal is implemented by applying two different types of linkersto hold the oligos 4210 onto the fibers 3806, namely cleavable 4214 andpermanent 4216 linkers. The clevable linkers 4214 dissolve during thedeprotection process while the permanent linkers 4216 do not. Most ofthe linkers are preferably permanent linkers 4216 such that only a smallpercentage of oligos 4210 are removed from the fiber 3806. The oligos4218 removed will be passed through various quality control sensors2008, such as for example a liquid chromotography column 4202 for puritymeasurement, with an ultraviolet light detector 4204 and a massspectrometer 4206 for identification.

FIG. 43 is an enlarged side view of another embodiment of a coatingmodule 4302. In this configuration, the coating module 4302 isprogrammed to synthesize one of multiple bases solutions 4304-4310, asselected by an operator, onto the fiber 3806. The base solutionspreferably would be oglios A, C, G or T. The module 4302 may stillcontain the detritylation 4004, activator 4006, capping agents 4010,wash-one 4012, oxidizer 4014, and wash-two 4016—solutions. However, themodule 4302 may additionally contain a bath for all bases 4304-4310instead of only a bath containing one base 4008 as described in relationto the first configuration 3820 (FIG. 40). The selector 3428 (shown inFIG. 34) selects one of multiple actuators 4312-4318 to push the fiber3806 into contact with one of the multiple base solutions 4304-4310,adding that base in the same process as described above. When adifferent base is desired, the extended actuator 4312, 4314, 4316 or4318 is retracted and another actuator 4312, 4314, 4316 or 4318 extendsthe fiber into contact with a different base solution 4304-4310. Thisprocess is repeated as often as desired to synthesize an oglionucleotideonto the fiber 3806. This type of coating module 4302 can be stacked asshown in FIG. 44, with fiber spools 3804, deprotection modules 3824, andmotor 3828 to lay the fibers 3806 into a plurality of fiber arrays 3826.

One application for the present invention is DNA synthesis, inparticular making every combination of a certain DNA length. Forexample, every combination of a 9 base long DNA fragment (oligo) wouldgenerate 262,144 different oligos (4 to the ninth power). Eight modulesper fiber could generate a 9-base oligo if the fibers are loaded intothe machine with one base already attached (see FIG. 17). However, tomake 262,144 stacks of 8-high modules would be daunting. But, with thisdevice, a relatively small set of modules can be arranged to multiplythe number of different combinations generated. For example, 256 fiberscan be passed through the upper hub with four-modules per fiber tosynthesis every combination of four bases on those fibers (256). If thelower hub is arranged the same way (256 fibers×4 modules), the systemwould synthesize 256, 9-base oligos simultaneously—a small subset of the262,144 combinations required. However, when a subset of fibers is made,the fibers can be cut, and the lower hub rotated to make a second subsetof fiber combinations. By repeating this process 256 times, 65,536combinations of a 9-mer will have been synthesized (255×256). Now, theplatform is rotated one fiber position and the whole process repeatedanother three times to synthesize every 9-mer combination of 262,144.

Various embodiments of the invention have been described. Thedescriptions are intended to be illustrative of the present invention.It will be apparent to one of skill in the art that modifications may bemade to the invention as described without departing from the scope ofthe claims set out below. For example, it is to be understood thatalthough the invention has described various geometries for the supportplate and the arrangement of the fibers and channels, other geometriesare possible and are contemplated to fall within the scope of theinvention. Further, although the invention has been illustrated withparticular reference to oligonucleotides and nucleic acid sequencing,any use for contacting at least two chemical species is contemplated tofall within the scope of the invention.

What is claimed is:
 1. A method for analyzing the contact between twochemical species comprising: contacting only a first surface portion ofan optical fiber with a first mobile chemical species; contacting only asecond surface portion of said optical fiber different to said firstsurface portion, with a second mobile chemical species different fromsaid first mobile chemical species, wherein said optical fiber has animmobilized chemical species immobilized on said first surface portionand said second surface portion; detecting whether binding occursbetween said immobilized chemical species and said first mobile chemicalspecies; detecting whether binding occurs between said immobilizedchemical species and said second mobile chemical species.
 2. The methodof claim 1, further comprising moving said first mobile chemical speciesand said second mobile chemical species toward said optical fiber. 3.The method of claim 2, wherein said moving comprises applying a motiveforce to said first mobile chemical species and said second mobilechemical species.
 4. The method of claim 3, wherein said motive force isselected from the group consisting of pumping, aspirating, gravity flow,electrical pulsing, vacuum, suction, capillary action, electro-osmosis,and combinations thereof.
 5. The method of claim 1, further comprisinglabeling said first mobile chemical species and said second mobilechemical species with a chemiluminescent moiety.
 6. The method of claim5, wherein said chemiluminescent moiety is selected from the groupcomprising of radioisotopes, chromophores, fluorophores, lumophores andcombinations thereof.
 7. The method of claim 1, further comprisingdirecting a light at an end of said optical fiber prior to saiddetecting.
 8. The method of claim 7, wherein said detecting comprisesdetecting excitation light emitted from where said binding occurs. 9.The method of claim 8, wherein said detecting further comprisesconverting said excitation light into an electrical signal that isproportional to said excitation light.
 10. The method of claim 1,wherein said detecting occurs at an optimum temperature.
 11. The methodof claim 1, further comprising changing a temperature of the opticalfiber over a predetermined range of temperatures such that thetemperature of said optical fiber will pass through an optimumtemperature for binding of said first mobile chemical species with saidimmobilized chemical species and said second mobile chemical specieswith said immobilized chemical species.
 12. The method of claim 1,further comprising immobilizing said immobilized chemical species alongsaid first surface portion and said second surface portion prior tocontacting said first surface portion.
 13. The method of claim 1,further comprising positioning said optical fiber on a support having afirst channel and a second channel, such that said optical fiber issubstantially perpendicular to said first channel and said secondchannel.
 14. The method of claim 13, wherein said positioning exposessaid first surface portion to said first channel and exposes said secondsurface portion to said second channels, where said first channel isconfigured to receive said first mobile chemical species and said secondchannel is configured to receive said second mobile chemical species.15. The method of claim 14, further comprising: disposing said firstmobile chemical species into said first channel; and disposing saidsecond mobile chemical species into said second channel.
 16. The methodof claim 1, wherein said detecting step further comprises directing alaser at a focusing lens that directs light at an end of said opticalfiber.
 17. A method for analyzing the contact between two chemicalspecies comprising: contacting only a first surface portion of anoptical fiber with a first mobile chemical species; contacting only asecond surface portion of said optical fiber different to said firstsurface portion, with a second mobile chemical species different fromsaid first mobile chemical species, wherein said optical fiber has animmobilized chemical species immobilized on said first surface portionand said second surface portion; and directing a light at an end of saidoptical fiber; detecting excitation light emitted from binding betweensaid immobilized chemical species and said first mobile chemicalspecies; and detecting excitation light emitted from binding betweensaid immobilized chemical species and said second mobile chemicalspecies.
 18. The method of claim 17, further comprising moving saidfirst mobile chemical species and said second mobile chemical speciestoward said optical fiber.
 19. The method of claim 18, wherein saidmoving comprises applying a motive force to each of said first mobilechemical species and said second mobile chemical species.
 20. The methodof claim 17, further comprising labeling said first mobile chemicalspecies and said second mobile chemical species with a chemiluminescentmoiety.
 21. The method of claim 17, further comprising changing atemperature of the optical fiber over a predetermined range oftemperatures such that the temperature of said optical fiber will passthrough an optimum temperature for binding of said first mobile chemicalspecies with said immobilized chemical species and for binding of saidsecond mobile chemical species with said immobilized chemical species.